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Researches on the method of the performance evaluation of government investment in public works project are mainly embodied in indicator system. However, these models do not attach importance to the applicability. So, it cause lack of suitable evaluation model for evaluate the projects of government investment in public works project. Therefore, this article in accordance with the characteristics of this investment in public works projects', combined the gray relational analysis method, fuzzy comprehensive evaluation method and stepwise discriminate analysis method with their respective advantages to develop a new algorithm-GFS algorithm. Using the GFS algorithm can do discriminate analysis for a new investment project. Practice shows that the GFS algorithm is assess a good effect. It can provide the theoretical basis for decision-making of senior government managers.