The ibtmp1 once created can’t be shrink by any method without restarting mysql service.
There are two ways to handle it:
Precaution : At the time of server start you should limit the size of this file as:
innodb_temp_data_file_path = ibtmp1:12M:autoextend:max:5G
where max 5G means this file size limits to 5GB.
Cure : If file already created you need to restart service:
SET GLOBAL innodb_fast_shutdown = 0;
Shutdown MySQL
remove ibtmp1
start MySQL.
Docs: https://dev.mysql.com/doc/refman/5.7/en/innodb-temporary-tablespace.html