The　rapid　development　of　the　transportation　industry　benefits　from　the　consumption　of　energy,　but　the　excessive　dependence　on　petroleum　fuels　makes　it　a　major　source　of　air　pollution.　In　order　to　achieve　green　and　high-quality　development　of　the　transportation　industry,　many　countries　are　committed　to　scientifically　evaluating　the　utilization　efficiency　of　clean　energy,　which　has　attracted　wide　attention　from　the　whole　society.　Significantly,　without　considering　the　diversity　and　complexity　of　pollutants,　indicators　used　in　previous　studies　were　unable　to　cover　all　pollutants　when　establishing　the　evaluation　index　system.　Meanwhile,　as　an　efficient　tool,　data　envelopment　analysis　(DEA)　is　extensively　used　when　it　comes　to　efficiency　evaluation.　However,　the　absolute　preference　of　existing　benevolent　and　aggressive　cross-efficiency　models　limits　its　application　scenarios.　To　address　the　challenges　above,　an　improved　flexible　cross-efficiency　DEA　model　is　proposed　considering　both　same　and　different　benevolence　coefficients　of　decision-making　units　(DMUs)　on　the　basis　of　pointing　out　the　inadequacy　of　the　previous　model.　The　concepts　of　consensus　coefficient　and　group　preference　are　introduced　in　the　aggregation　of　cross-efficiency.　Besides,　based　on　the　theory　of　undesirable　output,　the　consumption　of　nonclean　energy　is　taken　into　account　as　the　input　indicator　to　characterize　the　degree　of　pollution.　The　results　show　that　the　obtained　cross-efficiency　value　and　efficiency　ranking　of　clean　transportation　energy　change　sensitively　under　various　benevolent　coefficients.　There　is　an　important　practical　significance　to　consider　the　independent　preference　information　of　DMUs　for　the　evaluation　and　ranking　of　cross-efficiency.