As the most innovative and important institutes for the development of science and technology in China, due to various reasons, universities have not effectively achieved the commercialization of employee inventions. As a result, some universities have decided to conduct pilot projects with Mixed Ownership concerning patent rights for employee inventions under the framework of the Law of the People's Republic of China on Promoting the Transformation of Scientific and Technological Achievements (PTSTA) and Patent Law, namely transferring a portion of the rights to the employed inventors before the inventions are commercialized. The pilot reform has been backed by some local governments in China. This article systematically introduces and analyses this experimental system's theoretical and practical background, legal theory and policy logic. Southwest Jiaotong University (SWJTU) was selected as the subject of a case study to analyse its related progress and issues. This article also puts forward countermeasures and suggestions, such as establishing the comprehensive scientific research work orientation of the researchers in universities, preventing the legal risks of the transformation of employee inventions in universities, improving the capabilities of China's technology transfer institutions, and carrying out legislative practices, thereby providing references for the effective management of universities’ intellectual property and the reengineering of the employee invention system in China.