Not sure, what you mean, but when you set up the width and height in tilesource, it is used in tilemap
Properties: Tile Width and Tile Height
EDIT: Ah, I think you mean to have different tile size in tile map and different in tile source, right?
Could this answer your question:
Solutions for different tile sizes in map ?
Generally, would be great to know your use case, because having different tile sizes in tilemaps and tilesources looks conflicting - so maybe we could figure out some different solution to your specific problem? 