The confliction between the need of R&D expenditure and the limitation of R&D resources in certain time period is a serious issue facing both developing and developed countries. This paper deals with not only the mechanism of interaction between R&D, economy and education systems, also the mechanism and relation among basic research, applied research and development. Two system dynamics models were developed focusing on the above two problems respectively. And, through modeling and policy analysis, some new findings, such as the proper scale and growth-rate of national R&D expenditure, the relation between technology acquisition and self-developing R&D, the proper ratio of R&D expenditure, etc., were accomplished.