That ibdata1 isn't shrinking is a particularly annoying feature of MySQL. The ibdata1 file cannot actually be shrunk unless you delete all databases, remove the files and reload a dump.
This project could help to reduce the ibdata1 file size.
Backup all MySQL databases except some databases
Default to except mysql, information_schema, and performance_schema.
MySQL InnoDB basic tables
These are used in MySQL 5.6, and though are not required, will show errors in the error log if InnoDB tables are accessed and these tables are not present!
As you want to reclaim the space from ibdata1:
1.In /etc/my.cnf -> [mysqld], add "innodb_force_recovery = 4" to set InnoDB read-only. Make sure "innodb_data_file_path" had a true value.
2.Start MySQL service. Do a mysqldump of all databases except the mysql, information_schema, and performance_schema databases.(you can using mysql_dump_all_db.sh to do it, it's default to except for mysql, information_schema, and performance_schema databases)
3.Drop all databases except the above 3 databases.
4.Stop MySQL service. Delete ibdata1 and ib_logfile* files.
5.Delete innodb_index_stats.、innodb_table_stats.、slave_master_info.、slave_relay_log_info.、slave_worker_info.* files in mysql database folder(In MySQL 5.6 or higher, when you shutdown mysql, delete ibdata1, and start mysql back up, ibdata1 gets recreated. But these 5 tables are not recreated. Even if your deleted ibdata1, there are still in /usr/local/mysql/data/mysql, so need delete these files on yourself).
6.Remove "innodb_force_recovery = 4" from /etc/my.cnf. Start MySQL service.(When you start MySQL, the ibdata1 and ib_logfile* files will be recreated)
7.Restore databases from dump(See Step 2) and restore InnoDB basic tables(using the mysql_innodb_basic_tables.sql to restore).
8.Done. Restart MySQL service again to ensure error-free results. Thank you.
Testing in MySQL 5.6.25.