This worked for others in the past (just google pythonnet + pyinstaller) - perhaps you need to provide us with your versions of cpython, pyinstaller, .Net/Mono, pythonnet, spec file? On Monday, March 14, 2016, Simone Reis wrote:

How to make the distribution of python and pythonNet in a single exe file? I tried with py2exe and pyinstaler but always occur error in clr.pyd load. It only works when clr.pyd and Python.Runtime.dll are in the same folder and not compressed.

Thanks