Abstract: Considering time-lag between inputs and outputs in multiple phases as well as interdependence among various inputs and among diversified outputs, the study to solve problem on utilization effectiveness assessment of S&T resource in scientific research institutes is conducted in this paper based on the perspective of time-lag effect and interdependence effect. Firstly, a matrix analysis model and an assessment index system are constructed. Then, an assessment method considering time-lag effect and interdependence effect is proposed. Taking Chinese Academy of Sciences for example, an empirical study is conducted to assess such institute’s utilization effectiveness of S&T resource in the phases of knowledge transformation and achievement transformation. Furthermore, the assessment results are mapped into the matrix analysis model to analyze utilization effectiveness of S&T resource in depth. Moreover, the best allocation interval of S&T resource in two phases can be determined by sensitivity analysis. This study can provide a valuable decision reference for scientific research institutes to improve utilization effectiveness of S&T resource and explore the optimal path for S&T resource allocation.