2.8.14 to 3.0.0 2004-06-18
Version 3.0.0 is a major upgrade for SQLite that incorporates support for UTF-16, BLOBs, and a more compact encoding that results in database files that are typically 25% to 50% smaller. The new file format is very different and is completely incompatible with the version 2 file format.
That is the last documented SQLite "structure" change I could find.
Again the syntax for commands have changed, but that is just how data gets into and out of the database, once it is there, the structure is the same.