Abstract: The German experiences in R&D budget management and evaluation are introcluced, the management mechanism of expenditure allocation of three National Scientific Research Institutions (NSRIs) supported by German government is analyzed, and the management pattern of expenditure allocation of different NSRIs is abstracted. As a result, three recommendations for improving the S&T expenditure management of China are pointed out, namely, to strengthen the strategic management of national S&T strategy and policy, the supervision of S&T program implementation; to strengthen the S&T expenditure management of different NSRIs so as to improve the efficiency and effectiveness of expenditure utilization; to explore a new pattern integrating the growth of rewards with the performance of scientific research.