Agriculture has the dual attributes of being a carbon source and a carbon sink. The agricultural carbon compensation mechanism is important for increasing agricultural carbon sink and reducing agricultural carbon emissions. However, there is no specific entry threshold for the implementation of agricultural carbon compensation in China. Taking the two indicators of agricultural carbon sink level and agricultural carbon emission intensity as the basic indicators, and taking the regional average agricultural carbon sink level and the regional average agricultural carbon emission intensity as the baseline, we established the agricultural carbon compensation area selection process. According to the agricultural carbon compensation area selection process, the results obtained in Hotan Prefecture were reasonable. The result of selection accorded with the actual situation of agricultural carbon emission and agricultural carbon sinks in Hotan Prefecture.