The　Chinese　government　proposed　the　establishment　of　China　National　Ecological　Civilization　Pilot　Zone　in　2016　to　further　explore　the　coordinated　development　of　economy　and　environment.　Fujian,　Jiangxi,　and　Guizhou　provinces　were　selected　as　the　first　batch　of　pilot　zones.　After　years　of　exploration,　it　is　necessary　to　discuss　and　summarize　the　construction　progress　of　the　three　pilot　zones　from　the　perspective　of　the　city.　In　this　study,　first,　the　ecological　civilization　pilot　zone　construction　system　was　decomposed　into　an　economic　construction　subsystem　(ECS)　and　an　environmental　optimization　subsystem　(EOS).　Then,　a　two-stage　network　SBM　model　was　adopted　to　calculate　the　efficiencies　of　the　subsystems,　and　the　Kruskal-Wallis　test　was　used　to　measure　the　efficiency　difference.　Finally,　a　panel　data　regression　model　was　applied　to　explore　the　influencing　factors　of　both　subsystems.　The　results　show　that　the　ECS　efficiency　is　higher　than　that　of　the　EOS,　and　the　ECS　efficiency　in　Fujian　is　significantly　better　than　that　in　Jiangxi　and　Guizhou.　However,　there　is　no　significant　difference　in　EOS　efficiency　in　the　three　provinces.　Furthermore,　industrial　structure　and　population　agglomeration　have　a　significant　effect　on　ECS　efficiency,　environmental　regulation　has　a　significant　impact　on　EOS,　and　the　technology　level　has　a　significant　impact　on　both　subsystems.　Based　on　the　results,　policy　implications　for　improving　the　efficiency　of　the　two　subsystems　were　given　respectively.