This paper proposes a performance evaluation method of public administration departments based on the improved DEA algorithm, which solves the quality problem of performance evaluation of public administration departments and lays a foundation for the long-term development and performance improvement of public administration departments. The DEA model is the core to sort out the performance evaluation methods of public administration departments. From the perspective of DEA algorithm, whether DEA is effective is an important content that public administration departments must consider when carrying out performance administration, and public service satisfaction is the core parameter obtained by DEA algorithm. That is to say, by optimizing public services and improving service satisfaction, the public administration department can further improve the quality of performance evaluation. Therefore, we can carry out performance evaluation of public administration departments from the satisfaction of public services. The empirical research conclusion shows that according to the effective judgment theorem of DEA, it can be concluded that among the eight social security departments, there are five departments that can achieve DEA effectiveness, namely department 2, department 3, department 4, department 5, and department 6. There are three non-DEA valid ones, namely, department 1, department 7 and department 8. The public satisfaction and the total service cost will affect the performance quality to a certain extent, and only by balancing various influencing factors can the performance evaluation quality of the public administration department be maximized.