As already noted you can't shrink ibdata1 (to do so you need to dump and rebuild), but there's also often no real need to.
Using autoextend (probably the most common size setting) ibdata1 preallocates storage, growing each time it is nearly full. That makes writes faster as space is already allocated.
When you delete data it doesn't shrink but the space inside the file is marked as unused. Now when you insert new data it'll reuse empty space in the file before growing the file any further.
So it'll only continue to grow if you're actually needing that data. Unless you actually need the space for another application there's probably no reason to shrink it.