The purpose of this study is to evaluate and build mechanisms of boundary-spanning and compensation of Hsinchu Science Park by in-depth interviews. We found out the following results: (1) boundary-spanning mechanism of Hsinchu Science Park faced the problems of information asymmetry, slack regulations and implementation, and unstable boundary-spanning mechanisms. (2) mechanisms of compensation of Hsinchu Science Park suffered unstable and insufficient fund, unclear areas and contents of compensation, and underrepresentation of decision process. The study suggests the following actions: the authorities should (1) intensify Environmental oversight and information transparency, (2) maintain stable compensation funding and make it institutionalized, (3) pay attention to risk management.