Abstract: Agricultural products processing industry plays an important role in promoting industrial integration and economic growth. Based on the 12 agricultural product processing industry data in Anhui province from 2005 to 2016, this paper measures the Malmquist productivity index with DEA 2.1 software. It is found that the industry total factor productivity growth of agricultural product processing is mainly driven by technological progress. And it analyzes the factors affecting the total factor productivity of agricultural products processing industry by using panel data model, with Eviews 6.0 software. It is found that industrial agglomeration, enterprise scale, foreign direct investment, and investment in research and development have significant positive effect on total factor productivity growth. In the end, suggestions are presented with the conclusion:promoting the agricultural products processing industry agglomeration, fostering industrial clusters, optimizing the structure of the enterprise, increasing enterprise scale appropriately, making full use of foreign direct investment, increasing investment in research and development.