You really should take a thorough look at the documentation when dealing with a DBMS of this complexity.
Two important disk-based resources managed by the InnoDB storage engine are its tablespace data files and its log files. If you specify no InnoDB configuration options, MySQL creates an auto-extending 10MB data file named ibdata1 and two 5MB log files named ib_logfile0 and ib_logfile1 in the MySQL data directory.
Basically, the ibdata1 file contains the table data of your InnoDB tables. Specifying more than a single file would make sense in cases where you are using a different storage subsystem to store the second file for performance reasons or if you ran out of space for ibdata1 on its original partition and would want to have a simple add-on storage with a different storage file. Fixing the file size obviously has the effect of limiting the total amount of data which can be stored in InnoDB tables.
The ibdata1 file is probably auto-growing in your case, so it will inflate as more data is put into InnoDB tables. After records are deleted from InnoDB tables, the file will contain pages marked as "free" which could be used for future data, but the file itself is unshrinkable. If you have deleted larger amounts of data and need to shrink ibdata1, the only supported way goes through backing up the tables using
mysqldump and re-initializing your database - see this StackOverflow answer for details.