diff --git a/.appveyor.yml b/.appveyor.yml
index 0f9a15fa6e45..d97ef9c0f95f 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -1,4 +1,4 @@
-version: 3.0.0.99.{build}
+version: 3.1.0.{build}
 
 image: Visual Studio 2015
 platform: x64
diff --git a/R-package/configure b/R-package/configure
index 4fbf13f2a3a3..16a958315271 100755
--- a/R-package/configure
+++ b/R-package/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for lightgbm 3.0.0.99.
+# Generated by GNU Autoconf 2.69 for lightgbm 3.1.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -576,8 +576,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='lightgbm'
 PACKAGE_TARNAME='lightgbm'
-PACKAGE_VERSION='3.0.0.99'
-PACKAGE_STRING='lightgbm 3.0.0.99'
+PACKAGE_VERSION='3.1.0'
+PACKAGE_STRING='lightgbm 3.1.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1182,7 +1182,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures lightgbm 3.0.0.99 to adapt to many kinds of systems.
+\`configure' configures lightgbm 3.1.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1244,7 +1244,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of lightgbm 3.0.0.99:";;
+     short | recursive ) echo "Configuration of lightgbm 3.1.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1311,7 +1311,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-lightgbm configure 3.0.0.99
+lightgbm configure 3.1.0
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1328,7 +1328,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by lightgbm $as_me 3.0.0.99, which was
+It was created by lightgbm $as_me 3.1.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2389,7 +2389,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by lightgbm $as_me 3.0.0.99, which was
+This file was extended by lightgbm $as_me 3.1.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2442,7 +2442,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-lightgbm config.status 3.0.0.99
+lightgbm config.status 3.1.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
diff --git a/R-package/cran-comments.md b/R-package/cran-comments.md
index e6387f65a125..2270d9ddd18d 100644
--- a/R-package/cran-comments.md
+++ b/R-package/cran-comments.md
@@ -1,5 +1,63 @@
 # CRAN Submission History
 
+## v3.0.1 - Submission 1 - (November 15, 202)
+
+### CRAN response
+
+### Maintainer Notes
+
+This package was submitted with the following information in the "optional comments" box.
+
+```text
+Hello,
+
+I'm submitting {lightgbm} 3.1.0 on behalf of the maintainer, Guolin Ke. I am a co-author on the package, and he has asked me to handle this submission. We saw in https://cran.r-project.org/web/packages/policies.html#Submission that this is permitted.
+
+{lightgbm} was removed from CRAN in October for issues found by valgrind checks. We have invested significant effort in addressing those issues and creating an automatic test that tries to replicate CRAN's valgrind checks: https://github.com/microsoft/LightGBM/blob/742d72f8bb051105484fd5cca11620493ffb0b2b/.github/workflows/r_valgrind.yml.
+
+We see two warnings from valgrind that we believe are not problematic.
+
+==2063== Conditional jump or move depends on uninitialised value(s)
+==2063==    at 0x49CF138: gregexpr_Regexc (grep.c:2439)
+==2063==    by 0x49D1F13: do_regexpr (grep.c:3100)
+==2063==    by 0x49A0058: bcEval (eval.c:7121)
+==2063==    by 0x498B67F: Rf_eval (eval.c:727)
+==2063==    by 0x498E414: R_execClosure (eval.c:1895)
+==2063==    by 0x498E0C7: Rf_applyClosure (eval.c:1821)
+==2063==    by 0x499FC8C: bcEval (eval.c:7089)
+==2063==    by 0x498B67F: Rf_eval (eval.c:727)
+==2063==    by 0x498B1CB: forcePromise (eval.c:555)
+==2063==    by 0x49963AB: FORCE_PROMISE (eval.c:5142)
+==2063==    by 0x4996566: getvar (eval.c:5183)
+==2063==    by 0x499D1A5: bcEval (eval.c:6873)
+==2063==  Uninitialised value was created by a stack allocation
+==2063==    at 0x49CEC37: gregexpr_Regexc (grep.c:2369)
+
+This seems to be related to R itself and not any code in {lightgbm}.
+
+==2063== 336 bytes in 1 blocks are possibly lost in loss record 153 of 2,709
+==2063==    at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
+==2063==    by 0x40149CA: allocate_dtv (dl-tls.c:286)
+==2063==    by 0x40149CA: _dl_allocate_tls (dl-tls.c:532)
+==2063==    by 0x5702322: allocate_stack (allocatestack.c:622)
+==2063==    by 0x5702322: pthread_create@@GLIBC_2.2.5 (pthread_create.c:660)
+==2063==    by 0x56D0DDA: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
+==2063==    by 0x56C88E0: GOMP_parallel (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
+==2063==    by 0x1544D29C: LGBM_DatasetCreateFromCSC (c_api.cpp:1286)
+==2063==    by 0x1546F980: LGBM_DatasetCreateFromCSC_R (lightgbm_R.cpp:91)
+==2063==    by 0x4941E2F: R_doDotCall (dotcode.c:634)
+==2063==    by 0x494CCC6: do_dotcall (dotcode.c:1281)
+==2063==    by 0x499FB01: bcEval (eval.c:7078)
+==2063==    by 0x498B67F: Rf_eval (eval.c:727)
+==2063==    by 0x498E414: R_execClosure (eval.c:1895)
+
+We believe this is a false positive, and related to a misunderstanding between valgrind and openmp (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=36298).
+
+We have also added automated tests with ASAN/UBSAN to our testing setup, and have checked the package on Solaris 10 and found no issues.
+
+Thanks for your time and consideration.
+```
+
 ## v3.0.0.2 - Submission 1 - (September 29, 2020)
 
 ### CRAN response
diff --git a/VERSION.txt b/VERSION.txt
index 96533ec0ba84..fd2a01863fdd 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-3.0.0.99
+3.1.0