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The output loss between cooperation and non-cooperation strategies for areas 1–4 (2012–2016). • Environmental control parameters are set to manipulate multiple situations. • Non-equal proportional change of indices and preference coefficient for ports are proposed. • A distance formula of expected output for PM emission reallocation is provided. • New DEA models are applied to 11 Chinese main ports. The emission of particulate matter (PM) and other atmospheric pollutants in port operations and shipping have caused a huge negative impact on the environment. Consequently, how to evaluate the environmental efficiency of ports and put forward corresponding countermeasures on this basis is becoming a more important issue than ever before from the perspectives of the government, academia, and society. We construct three data envelopment analysis (DEA) models to evaluate the environmental efficiency of ports under the circumstances of environmental control, non-environmental control and PM emission through inter-ports cooperation. The innovation of the DEA models constructed in this paper lies in: (1) Setting environmental control parameters to uniformly manipulate the situations of environmental control and non-environmental control, etc.; (2) Allowing non-equal proportional change of input index, expected output and non-expected output index; (3) Setting preference coefficients for ports to admit favorable decisions; (4) Providing a distance formula of expected output for PM emission reallocation. Further, data from 11 major ports in China are collected to compare the expected output under different PM emission standards assuming the situation of environmental control and non-environmental control, port cooperation, and non-cooperative sewage discharge. The empirical results show that: (1) Ports in the eastern China (Shanghai, Ningbo, and Nanjing) have higher port efficiency; (2) Port cooperation can improve the overall expected output but it will lose its edge with the improvement of PM emission standards. (3) Ports follow the same trend of output loss regardless of favorable decisions. In the end, the author makes a summary, puts forward relevant policy suggestions and makes the recommendation for future research. [ABSTRACT FROM AUTHOR]