Abstract In an open creative environment, R&D cooperation between enterprises, high educations and scientific institutes is a must way to improve national technological innovative ability. It is not only a technological innovation, but also a kind of information activity. The essence of R&D cooperation is a process to optimally allocate information resources and reintegrate innovative factors. Information resources allocation in R&D activities is multi-looped, nonlinear, high degree, and hard to quantify, which are the characteristics of system dynamics. By the application of system dynamics, this article conducts a qualitative and quantitative research on mechanism of information resources allocation in industry-academia-research(IRA) R&D cooperation, analyzes the causality of all subject, draws a system dynamics flowchart of information resources allocation, and builds a system dynamics model. This model contains 5 state variables, 7 rate variables, 15 instrumental variables and 8 constant, covering processes of development and utilization, input and output, demand and supply of information resources. The model reflects the realization process of the information resources allocation in R&D cooperation. Based on this model, this article simulates the implementation of information resources allocation of our country in 2010-2025 and predicts the trend of our information resources allocation within 15years. The result shows the influence on the allocation of the following four factors: performance of government macro-management, perfection degree of market mechanism, service level of technological agency and distribution benefit among all cooperation subjects. This article provides a good solution for enterprises, high educations and scientific institutes to improve the utilization benefit of information resources in R&D cooperation.