In applied universities, innovation and entrepreneurship education (IEE) has entered a new era of comprehensive integration of professional education. However, as a novel educational activity, the evaluation of professional innovation integration still lacks reasonable appraisal standards. This article is based on the basic theory of the Kirkpatrick evaluation model, combined with the innovation and entrepreneurship practice of China's applied universities. This study initially constructs an index system for professional innovation integration in applied universities, estimates and ascertains the weights of different indicators using the Delphi and analytic hierarchy process approach, and thereafter, builds an index system for professional innovation integration in applied universities, which comprises of 4 primary indicators, namely: reaction layer, learning layer, behavior layer, and achievement layer, supported by 9 secondary indicators and 23 tertiary indicators.