The economy of China has turned to the stage of high-quality development. In this sense, the connotation of regional innovation capacity should reflect more aspects, such as better economic effectiveness, people-centered philosophy of development and better living conditions. This study aims at establishing the evaluation index system of regional innovation capacity under high-quality perspective. Then the dynamic evaluation method based on gray correlation degree and TOPSIS is improved. And the improved method is applied to evaluate the regional innovation capacity under high-quality development perspective. The results show that: 1) The regional innovation capacity of Jiangsu, Zhejiang, Shanghai and Guangdong under high-quality development perspective is better than other regions, while the regional innovation capacity of Beijing-Tianjin-Hebei is imbalanced. Regional innovation capability of Fujian, Shandong, and Hainan from a high-quality perspective is at the middle and lower levels. 2) From the perspective of development trends, the gap of regional innovation capacity between Beijing, Jiangsu, Zhejiang, Shanghai, Guangdong and Fujian, Hebei, Shandong is gradually narrowing. 3) An in-depth analysis of the regional innovation capability of the eastern provinces and cities from the perspective of high-quality development through different dimensions shows that Beijing, Guangdong, Jiangsu perform well in all dimensions, while Fujian and Hainan need to pay more attention to innovation input and the creation of a better innovation environment to enhance innovation output and promote innovation effectiveness. At last, based on above analysis, relevant policy recommendations are proposed.