This paper describes the connotation and characteristics of research-oriented university and its innovation and entrepreneurship education. Based on the level，characteristics，objectives，content，and structure of innovation and entrepreneurship education in research-oriented universities，this paper analyzes the influencing factors of comprehensive evaluation index design which are mainly involved in government level，college level，students level and social level. This paper constructs the quality evaluation index system and analyzes the quality of innovation and entrepreneurship education in research-oriented universities with the help of improved BP neural network model. Finally，this paper makes a comparatively good evaluation results from the tow aspects of social reliability and validity.