Objective To explore status and problems of patents management of pilot institutions in intellectual property in Shanghai health system, and to make suggestion on policy adjustment. Methods The quantitative analysis was performed. The questionnaire for 57 patent administrative staff and 287 research investigators were applied in all 20 institutions. The institutions included 17 pilot institutions in intellectual property (pilot group) and 3 normal institutions (non-pilot group). The questionnaire consisted of basic information of subjects, patents training and management, patents knowledge, patents information utilizing, transfer of patents, and implement of patents. Results The responsibilities of administrative staff were mainly focused on patent application (73.7%). Compared to non-pilot group, the administrative staff from pilot group had better academic degree, professional title, education background, and qualification. There was significant difference of number of attending training of patent knowledge between pilot group and non-pilot group （P＜0.05）. The training which mostly wanted for administrative staff in pilot group was “patent evaluation”; and for research investigators in both groups was “patent application”. The scoring rate of the exam for basic patent knowledge were 52.4% in administrative staff and 32.3% in research investigators. There were 41.5% research investigators never knew foreign patent data base. There were 73.7% of administrative staff and 67.6% of research investigators asked for government guidelines which should be specific for the patent management in health care system; and 68.4% of administrative staff and 65.5% of research investigators needed the assistance of patent evaluation during the transfer of patents. Conclusion The government should strengthen the awareness and training; improve the system and mechanism of patent management; accelerate the education for versatile professionals with knowledge of intellectual property and medicine; increase production and quality of patents; and establish the platform for transfer of medical and pharmaceutical patents.