In terms of the panel data of listed companies in China’s A-share manufacturing industry from 2007 to 2018, using SFA method to measure and decompose the growth of total factor productivity of enterprises. The impact of heterogeneous enterprise leverage ratio on the total factor productivity and its structure of the manufacturing industry was tested. Leverage ratio does not significantly affect the growth of total factor productivity, technical efficiency and resource allocation efficiency of enterprises, but deleveraging significantly promotes the progress of frontier technology, while increasing leverage significantly improves scale efficiency. The consistent estimation results were obtained by changing control variables, leverage ratio measure, transforming samples and selecting instrumental variables. Further test and analysis show that firm heterogeneity also affects the effect of leverage ratio on the growth of TFP and its structure to varying degrees.