The article constructs the conceptual model for national innovation system based on science and Technology resource flows from the whole and system perspective. Through the system simulation and computational experiment, it discusses the fluctuant trend of Chinese science and technology papers and patents with different methods adopted to allocate resources of financial capacity, manpower and information in science and technology between university, scientific research institution and enterprise. The paper aims at providing reference for government departments for making policy about the optimal allocation of science and technology resources.