The operation mode of scientific research incentive mechanism in West China Hospital of Sichuan University is closely connecting individual needs with organizational objectives, and coordinating and adjusting again through communication and feedback. It can play an incentive role continuously and actively promotes the development of hospital scientific research. But the incentive mode, research funding management, research output rate, strengthening of effective communication and other aspects need to be constantly optimized and improved. Based on Porter Lawler’s comprehensive incentive theory, this paper explores and summarizes the operation mode of scientific research incentive mechanism in West China Hospital of Sichuan University. Finally, the paper puts forward suggestions, which aims to provide reference for the construction of scientific research incentive mechanism in large general hospitals.