Recently,　China　advanced　a　policy　of　establishing　a　protected　area　system　with　national　parks　as　the　main　body,　and　so　the　development　of　protected　areas　has　entered　a　transitional　period.　However,　to　promote　the　coordinated　development　of　economic　construction　and　ecological　protection　of　protected　areas,　their　management　needs　to　be　more　comprehensive　and　refined.　Therefore,　a　more　quantitative　and　refined　spatial　planning　and　management　method　for　protected　areas　is　urgently　needed.　This　study　took　Sanjiangyuan　National　Park　as　the　research　object　and　considered　the　three　biodiversity　elements　of　species,　ecosystems　and　landscape.　The　maximum　entropy　(MaxEnt)　model,　Integrated　Valuation　of　Ecosystem　Services　and　Tradeoffs　(InVEST)　model,　and　Fragstats　software　were　used　to　determine　the　areas　with　highly　suitable　species　habitat,　areas　of　high　ecosystem　service　value　and　areas　of　high　landscape　diversity.　Based　on　these　areas,　Marxan　software　was　used　to　calculate　the　irreplaceability　value,　identify　the　boundary　of　Sanjiangyuan　National　Park　and　clarify　the　gaps　of　the　existing　Sanjiangyuan　National　Park　in　the　space.　We　suggest　that　at　least　18,569　km(2)　of　the　eastern　part　of　the　Sanjiangyuan　Region　with　a　high　irreplaceability　value　should　be　included　in　the　existing　Sanjiangyuan　National　Park.　Moreover,　the　first-level　zones　were　also　classified　based　on　irreplaceability,　and　the　second-level　functional　zones　were　classified　by　K-means　clustering　based　on　the　evaluation　of　ecological　vulnerability　and　economic　construction　suitability.　The　first-level　zones　include　＂core　conservation　zones＂　and　＂general　control　zones＂,　which　had　areas　of　71,758.20　km(2)　(57.99%)　and　51,980.13　km(2)　(42.01%),　respectively.　The　core　conservation　zoneswere　further　zoned　into　primary　vulnerable　zones　and　secondary　vulnerable　zones.　The　subzones　of　the　general　control　zones　are　multifunctional　and　they　are　tourism-grazing-living　zones,　grazing-living　zones,　tourism-living　zones,　tourism　zones　and　other　areas.