This study analyzes the academy-run enterprises (AREs) in China, which have played an important role in the development of high-tech industries in China, but have rarely been deeply addressed in previous studies. The AREs, despite ostensibly sharing some similarities with the academic spin-offs (ASOs) found in other countries, have distinct historical origins and characteristics in China. In this study, we try to clarify the distinct features of Chinese AREs, particularly in terms of their relationship with their mother institutions, using questionnaire survey data collected from 102 AREs and subsequent follow-up interviews with the ARE managers. This study finds that, while the AREs have enjoyed an exclusive right to exploit various assets of their mother institutions, they have suffered from the interventions of the mother institutions and ambiguous property right arrangements with the mother institutions. More recently, AREs have begun to evolve in response to the changing environment. Furthermore, recently initiated reform measures are expected to accelerate this evolution. Using the survey results, this study assesses the short-term and long-term impact of the reform on Chinese AREs, and the subsequent impact on the academia-industry relationship and the national innovation system (NIS) in China.