> I noticed that caches on Lib/encodings/__init__.py and codec_search_cach of PyInterpreterState are the places holding the refs. I removed those caches and number went do to.

Good Catch, Paulo.
IMHO, caches is useful in codecs(it's improve the search efficiency).

I have two humble idea:
1. Clean all item of codec_search_xxx in `Py_Finalize()`;
2. change the refcount mechanism(in this case, refcount+1 or refcount+2 make no differenct);