With the initial establishment of the market economic system in China, non-profit national S&T institutes are enjoying more and more resources as they play an increasingly important role in science and technology development. By using the two economic managerial methods of expenditure budget control and performance evaluation, S&T administrators could have effectiveness of various kinds of economic management in the institutions, improve the efficiency and returns of their economic resources and raise their comprehensive managerial level. In addition, the methods could help them further perfect their input and output system so as to maintain an innovation and development momentum. The authors make discussions and offer suggestions on the two economic levels.