Due　to　the　existing　inverse　data　envelopment　analysis　(DEA)　methods　fail　to　address　the　problem　of　the　optimization　of　resource　allocation　in　the　two-stage　production　structure　containing　undesirable　outputs,　this　study　proposes　a　new　inverse　DEA　method　with　undesirable　output　within　the　two-stage　production　structure　for　analyzing　the　optimization　of　environment　resource　allocation.　Then,　a　new　inverse　DEA　method　with　frontier　changes　and　undesirable　output　in　two-stage　production　structure　is　further　developed　by　relaxing　the　constraint　of　unchanged　production　frontier,　which　can　be　used　to　analyze　the　optimization　of　environment　resource　allocation　in　two-stage　production　structure　for　the　future.　These　two　proposed　methods　open　the　＇black　box＇　of　the　complex　internal　structure　in　two-stage　production　structure　and　provide　more　comprehensive　and　accurate　information,　which　are　useful　tools　for　resource　allocation　and　formulation　and　planning　of　development　goals.　Finally,　an　empirical　study　relating　to　China＇s　industrial　two-stage　system　is　given　to　verify　the　rationality　and　effectiveness　of　the　methods　in　this　study.　©　2023　Systems　Engineering　Society　of　China.　All　rights　reserved.