The DEA-Malmquist index method was used to measure the agricultural total factor productivity（TFP） of Chongqing from 2006 to 2017, and the correlation between agricultural TFP and regional economy was analyzed by grey correlation method. The results showed that the TFP index of agriculture in Chongqing was greater than 1 from 2006 to 2017, with an average annual growth rate of 4.74 %. Among them, the fastest growth rate of agricultural TFP was 13.82 % in 2013～2014. In the TFP index composition, the average annual growth rate of agricultural technology progress is 3.47%, and the annual growth rate of technical efficiency is 1.27%. Technological progress is the main driving force of TFP growth in Chongqing. The relationship between total agricultural factors and agricultural economic growth in Chongqing is in descending order from mechanical power, fertilizer, energy, labor force and land.From 2006 to 2017, with little fluctuation in land and labor force, the continuous increase in mechanical power, fertilizer and energy effectively promoted the growth of rural economy.