The chain model of evolutionary can visually describe and study the process of economic activities, as to supervision on research funds of colleges and universities, we build the Government's supervision of university research funding with the inter-grey non-symmetric evolutionary game chain model, though simulating the process, we revealed the illegal use of scientific research, as well as proposed recommendations for the rational use of research funding to strengthen supervision of them, it provided new ideas and methods to improve the efficient use of research funding.