The innovative R&D activities of universities undertake the social resource conversion function of transforming scientific research resources into multiple scientific research outputs, and their scientific research capability largely determines the level of national scientific and technological innovation. This paper firstly establishes DEA-BP neural network comprehensive evaluation model, selects relevant input-output evaluation indexes of universities, then evaluates the efficiency of R&D innovation activities of universities in western region from 2011 to 2020 by DEA method, finally uses BP neural network to simulate and predict the R&D innovation efficiency, and based on the evaluation results, puts forward a A series of suggestions were made based on the evaluation results.