I found the solution myself.
you have to start matlab directly from conda while the correct environment ist activated. (type "matlab" in conda).
And add this to you matlab script:
pathofDocument = fileparts(which('custompythonscript.py'));
if count(py.sys.path,pathofDocument) == 0
insert(py.sys.path,int32(0),pathofDocument);
end
I hope that this will help someone out there.