Different evaluation methods and analysis theory has different emphasis and foothold. Combined with peer-reviewed method, analytic hierarchy process and matter-element analysis theory can not only supply shortage each other but also play to their respective advantages properly, which make the comprehensive evaluation more scientific, objective and accurate. Through the analysis of these theories, combine with the expert evaluation method, improve the matter-element and hierarchical evaluation model, and give an example of it. This model can well solve the problem of project integration for more projects funded and knowledge sharing executing between researchers in project research process.