The　hierarchical　diagnosis　and　treatment　system　is　at　the　core　of　China＇s　new　round　of　medical　reforms.　We　evaluated　the　operational　efficiency　of　the　hierarchical　diagnosis　and　treatment　system　in　primary　medical　and　health　institutions　in　Fujian　Province.　We　used　the　data　envelopment　analysis　algorithm　to　calculate　＇input-output＇　data　from　2016　to　2018　and　established　an　index　system.　Regarding　results　for　efficiency　value,　the　implementation　efficiency　of　Xiamen　was　1.15,　Fuzhou　was　1.10,　Zhangzhou　was　1.09,　Ningde　was　1.06,　Quanzhou　was　0.98,　Nanping　was　0.96,　Putian　was　0.94,　Longyan　was　0.92,　Sanming　was　0.86,　and　Pingtan　was　0.82.　There　were　few　and　insufficient　doctors　providing　services;　in　2018,　the　number　of　practicing　(assistant)　doctors　per　1000　permanent　residents　in　primary　medical　institutions　in　Fujian　was　only　0.799.　Outpatient　and　emergency　service　visits　were　increasing　yearly;　in　Fujian,　they　increased　by　8.39%　from　2016　to　2018.　From　the　incentive　system　of　hierarchical　diagnosis　and　treatment,　the　redundancy　rate　of　each　city　was　generally　high,　with　only　that　of　Nanping　(3.28%)　and　Longyan　(0.00%)　being　lower.　In　general,　for　the　hierarchical　medical　system　to　succeed,　we　should　start　with　innovative　management　policy　and　explore　ways　to　adapt　to　local　circumstances　(such　as　population,　economy,　etc.).