Promoting the transformation of international trade development momentum from traditional comparative advantage to human capital advantage is of great significance for promoting the upgrading of global value chain and enhancing the international competitiveness of manufacturing industry. This paper uses the matching data of manufacturing enterprise data and city panel data to discuss the impact of human capital on the upgrading of manufacturing value chain and its mechanism. The results find that the expansion of human capital can promote the upgrading of manufacturing value chain by promoting technological innovation, upgrading the structure of manufacturing industry and the servitization of industrial structure, and strengthening the effect of urban agglomeration, which depends on the type of enterprise trade, region, city and type of enterprise ownership. Large cities above type II have significantly benefited from the externality of human capital in the rise of export value of manufacturing industry, while small and medium-sized cities, especially small cities, have not obtained obvious advantages in the rise of export added value in the externality of human capital.