To promote sustainable development of agriculture, it is critical to reduce carbon sources and increase carbon sinks in farmland ecosystem by rationalizing the measures of agricultural management. This calls for scientific evaluation of net carbon sink (NCS) and its spatiotemporal evolution of farmland vegetation in a region. Taking 38 districts/counties of Chongqing, China as objects, this paper estimates the farmland vegetation NCS of Chongqing, based on statistics of crop yields and farmland inputs in 2000-2017. Then, geographical techniques were employed to analyze the features, regional difference and spatial evolution of NCS in Chongqing and its districts/counties. The main results are as follows: (1) From 2000 to 2017, the NCS and NCS strength (NCSS) of farmland vegetation in Chongqing both increased with fluctuations. The carbon sink, carbon emissions and carbon absorption increased across the board. The evolution of farmland vegetation can be divided into a wavy decline phase from 2000 to 2006, and a gradual increase phase from 2006 to 2017. (2) The source/sink structure of farmland vegetation in Chongqing remained stable in 2000-2017. The main sources are pesticide and tillage, and the main sinks are corn, rice, vegetables and oil crops. (3) In term of space, the farmland vegetation NCS and its center of gravity concentrated in the west zone and northeast zone. In general, the farmland vegetation of Chongqing boasts a strong carbon sink function; the west zone and northeast zone have the highest farmland vegetation NCSs; the west zone is the demonstration region of NCSS improvement.