Abstract: 【Objective】 Based on the intercropping pattern in four prefectures of southern Xinjiang, this paper aims to construct the index system of agricultural production efficiency and calculate the comprehensive efficiency, technical efficiency and scale efficiency of agricultural production. 【Methods】 Based on 22-year panel data from 2000 to 2021, DEA model method was used to analyze agricultural production efficiency and evaluate the input-output effect of agricultural factors. 【Results】 The agricultural production efficiency of the four prefectures was at a high level, which could effectively promote the rapid progress of agriculture in Xinjiang, but it was still a DEA non-active area.There were many redundant agricultural input factors, which did not achieve the best economic and social benefits. (2) The efficiency of the input index was in the order from good to bad: the number of rural labor force > the sown area of crops > the total power of agricultural machinery > rural electricity consumption > the amount of fertilizer applied > the amount of agricultural plastic film used > the expenditure on agriculture, forestry and water affairs. (3) The scale income was generally in the increasing stage, and the regional production potential could be continuously tapped 【Conclusion】 There is a "surplus" of agricultural input factors in the four prefectures in southern Xinjiang, and government departments should strengthen macro-control, release the resources that have been over-invested in the primary industry, optimize the rational allocation of resources, and enhance the efficiency of inputs and outputs. They should do: (1) Rationally adjust the proportion of agricultural financial input and distribution, and optimize the rational allocation of resources, improve the efficiency of agricultural financial expenditure; (2) Guide the transfer of labor to secondary and tertiary industries.(3) Continuously promote the reduction of fertilizer and pesticide dosage and increase efficiency. (4) To improve the level of agricultural equipment and information technology.(5)Adjust planting structure and planting mode to improve the efficiency of land output.