Based on the panel data of 37 counties in Chongqing from 2000 to 2016, this paper uses the sequential DEA method to measure the change of total factor productivity in Chongqing. Based on this, this paper discusses the time evolution of Chongqing’s agricultural total factor productivity growth and examines the impact of urbanization and industrialization on the growth of agricultural total factor productivity systematically from both theoretical and empirical level. Firstly, the results suggest that the total factor productivity of Chongqing has increased from 2000 to 2016. After 2007, the growth of agricultural total factor productivity in Chongqing is more obvious, and different regions in Chongqing show obvious spatial imbalance. Secondly, the empirical results of the dynamic panel model show that urbanization has a significant positive impact on agricultural total factor productivity growth, and so does industrialization. Finally, the research also finds out that infrastructure, education and financial development all have a significant positive impact on agricultural total factor productivity growth while industrial structure has a significant negative impact on it.