The National Graduate Education Comprehensive Fees Policy has been in operation for more than five years since the fall semester of 2014, which is long enough to evaluate the effectiveness of the policy. Base on the existing research results, this paper proposes to adopt the core index of graduate students' scientific research ability--the level and quantity of published papers to evaluate the implementation effect of this policy, take GF University as an example to analyze the construction of the university's award and scholarship system, and make quantitative analysis of the academic graduate students' published papers. It finds that the implementation effect of scholarship system is not obvious. Therefore, this paper analyzes the reasons and puts forward the relevant countermeasures.