The innodb_file_per_table option is enabled by default as of MySQL 5.6.6.

To set the innodb_file_per_table option at startup, start the server with the --innodb_file_per_table command-line option, or add this line to the [mysqld] section of my.cnf:

[mysqld]
innodb_file_per_table=1

You can also set innodb_file_per_table dynamically, while the server is running:

SET GLOBAL innodb_file_per_table=1;

With innodb_file_per_table enabled, you can store InnoDB tables in a tbl_name.ibd file. Unlike the MyISAM storage engine, with its separate tbl_name.MYD and tbl_name.MYI files for indexes and data, InnoDB stores the data and the indexes together in a single .ibd file. The tbl_name.frm file is still created as usual.

If you disable innodb_file_per_table in your startup options and restart the server, or disable it with the SET GLOBAL command, InnoDB creates new tables inside the system tablespace.

You can always read and write any InnoDB tables, regardless of the file-per-table setting.

To move a table from the system tablespace to its own tablespace, change the innodb_file_per_table setting and rebuild the table:

SET GLOBAL innodb_file_per_table=1;
ALTER TABLE table_name ENGINE=InnoDB;