As the core engine for cultivating new quality productive forces, innovation plays an increasingly prominent role in promoting the high-quality development of foreign trade. In order to fully release the innovation momentum and improve the international competitiveness of enterprises in the transformation and upgrading of foreign trade, it is still necessary to clarify the internal logic of the effect of innovation on export product quality and its heterogeneous effects. Under the framework of the heterogenous productivity quality model, and based on the matching data of China industrial enterprise database, China customs database and patent database from 2001to 2013，this paper analyzes the impact of innovation on the quality upgrading of enterprises' export products and its mechanism. The results show that innovation has a positive impact on the quality upgrading of export products, especially for enterprise with high-level innovation activities, of high-level intellectual property protection as well as in medium technology industry. At the same time, the results of mechanism analysis show that innovation can promote the quality upgrading of export products by improving enterprise profits and profitability, enabling enterprises to invest in intermediate products and human capital both with higher quality. The above research is of great significance to further understanding the innovation enabling mechanism, promoting the quality and efficiency of foreign trade, and accelerating the formation of new quality productive forces.