From the perspective of urban innovation capability, this paper selects the data of 283 prefecture level cities in China from 2001 to 2017 to analyze the impact of the improvement of urban innovation capability on the export trade of high-tech products from a theoretical and empirical perspective. The results show that the improvement of China’s urban innovation ability has a significant positive impact on the total export trade and export margin of high-tech products, and has a relatively large impact on the export expansion margin. At the same time, the impact of the improvement of urban innovation capability on the export of high-tech products shows significant regional differences. The positive impact on the export trade of high-tech products is mainly reflected in the central and western regions, with little impact on the eastern region, and only reflected in the expansion margin. In addition, urban innovation capability has a relatively large role in promoting the export trade of electronic and communication equipment manufacturing industry and computer and office equipment manufacturing industry, while it has a small role in promoting the export trade of aerospace and equipment manufacturing industry, and this impact is mainly reflected in the intensive margin.