This paper is a summary of the China's Basic and Clinical Medicine Research & Innovation System, a subproject of the major advisory project titled the National Health and Medical & Health Industry Development Strategy that was launched by the Chinese Academy of Engineering. This paper conducted an in-depth analysis of the medical research management and system construction of major world powers and of the major obstacles that hinder innovation in China's medical science and technology. It then put forward a list of suggestions that include strengthening the top-level design of medical research, restructuring the medical research system, increasing research funding, improving the evaluation system, integrating shared resources in medical science and technology, and accelerating the translation of medical research achievements.