With the exception of spatial indexes, InnoDB indexes are B-tree data structures. Spatial indexes use R-trees, which are specialized data structures for indexing multi-dimensional data. Index records are stored in the leaf pages of their B-tree or R-tree data structure. The default size of an index page is 16KB. The page size is determined by the innodb_page_size setting when when the MySQL instance is initialized. See Section 15.8.1, “InnoDB Startup Configuration”.

When new records are inserted into an InnoDB clustered index, InnoDB tries to leave 1/16 of the page free for future insertions and updates of the index records. If index records are inserted in a sequential order (ascending or descending), the resulting index pages are about 15/16 full. If records are inserted in a random order, the pages are from 1/2 to 15/16 full.

InnoDB performs a bulk load when creating or rebuilding B-tree indexes. This method of index creation is known as a sorted index build. The innodb_fill_factor variable defines the percentage of space on each B-tree page that is filled during a sorted index build, with the remaining space reserved for future index growth. Sorted index builds are not supported for spatial indexes. For more information, see Section 15.6.2.3, “Sorted Index Builds”. An innodb_fill_factor setting of 100 leaves 1/16 of the space in clustered index pages free for future index growth.

If the fill factor of an InnoDB index page drops below the MERGE_THRESHOLD, which is 50% by default if not specified, InnoDB tries to contract the index tree to free the page. The MERGE_THRESHOLD setting applies to both B-tree and R-tree indexes. For more information, see Section 15.8.11, “Configuring the Merge Threshold for Index Pages”.