Abstract: In view of the lack of quantitative assessment of process configuration efficiency from a system perspective in the current machine picking process optimization, the machine picking process system is regarded as a system with input and output, and the machine picking production inputs and process configuration are used as input indicators, and the output level of machine picking processing quality and lint yield are used as output indicators, and a SE-SBM（Super Efficiency Slacks-based Measure） process configuration efficiency evaluation model was established. Taking nine machine picked cotton processing lines of a cotton processing enterprise in Xinjiang as an example, the process configuration efficiency was evaluated and compared through data collection and calculation using DEA-Slover 5.0 software, and then the improvement direction and amount were determined based on the conclusions obtained, and targeted suggestions were made. The index system and evaluation method constructed in this paper can be used to assess the process configuration efficiency of different machine picking cotton processing lines, which can provide decision reference for implementing machine picking cotton processing process design and optimization improvement.