Environmental pollution, waste of resources, economic recession, political games and other problems force human beings to take the path of sustainable development. Promoting the sustainable development of education has become the mainstream recognition of all countries in the world. Based on the background of sustainable development, this paper studies the evaluation of graduate education. Firstly, the thesis is based on the evaluation of the effect of integrating red gene into graduate education. Secondly, the evaluation index system of the graduate education effect is constructed by using the expert group decision-making method, and the analytic hierarchy process is applied to determine the index weight. Finally, the paper uses the comprehensive index method to get the result of the educational effect evaluation. Through the empirical analysis, the following conclusions are drawn: (1) The evaluation index system of the graduate education effect can be carried out in five aspects: A academic discipline construction, B daily management, C party and league construction, D academic integrity, E curriculum ideology and politics. (2) The index weight of graduate student effect evaluation has typical heterogeneity. The lowest weight value is 18.16%; The highest weight is 24.25%. (3) The average score of graduate education effect evaluation of the university in the survey sample is 1.00996, which is in the interval [1.0,1.1], corresponding to the grade Ⅱ, indicating a very good educational effect.