In the process of airport operation research, non-expected output factors are often neglected. Meanwhile, the effective DMU can not be ranked further in researching the efficiency of airport operation. Therefore, this paper established Super-SBM model and selected 30 major airports in east China in 2017 as samples. This paper also divided the airport operation into two stages of airport service and passenger service. Then, it evaluated the airport operation efficiency and gave the ranking of the airports. Simultaneously, the necessity of introducing non-expected output and the advantage of Super-SBM model in solving the efficiency of airport operation was proved by the comparison and verification of calculation examples. It is found that the DEA-efficient airports were further differentiated. After introducing non-expected output, most of the airport operation efficiency of the sample airports has increased. Five airports have changed from DEA-inefficiency to DEA-efficiency and the operational efficiency of small airports has been significantly improved. Based on the Super-SBM model, this paper, researching airport operation efficiency from different stages, can provide guidance and help for airport operation.