Entrepreneurship education activities in colleges and universities play an important role in improving students’ innovation ability. Therefore, this paper has important practical value to evaluate the innovation and entrepreneurship ability of college students. At present, most studies use qualitative research methods, which is inefficient. Even if quantitative analysis is adopted, it is mostly linear analysis, which is inconsistent with the actual situation. In order to improve the application level of genetic algorithm to the innovation and entrepreneurship ability of universities based on BP neural network, this paper studies the evaluation model of innovation and entrepreneurship ability of universities. Based on the simple analysis of the current situation of university innovation and entrepreneurship ability evaluation and the application progress of BP neural network, combined with the actual situation of university innovation and entrepreneurship, this paper constructs the innovation and entrepreneurship evaluation index, uses BP neural network to build the evaluation model, and uses genetic algorithm to optimize and improve the shortcomings of BP neural network. Then, the experimental analysis and application design are carried out. The results show that the improved algorithm is basically consistent with the predicted value, small error, and fast convergence. When it is used in the evaluation of innovation and entrepreneurship ability, quantitative analysis results can be obtained, which provides a certain reference for the development of enterprises.