Regional scientific and technological innovation capability has become the decisive factor of regional comprehensive competitiveness. Scientific and comprehensive evaluation of regional scientific and technological innovation capability is helpful to improve the regional economic level. The evaluation index system of regional scientific and technological innovation capability of China is established from four dimensions of innovation input capability, innovation output capability, technology transformation capability and innovation environment support capability. Considering the influence of index priority, the incomplete index order relationship correction method is adopted, analytic hierarchy process and entropy method are used to weight the evaluation indexes, and then the modified TOPSIS （technique for order preference by similarity to ideal solution）method is used for comprehensive evaluation. Finally, four representative provinces and cities of Shaanxi, Beijing, Henan and Liaoning are selected to comprehensively evaluate their scientific and technological innovation ability, so as to verify the effectiveness of the evaluation method.