Scientific　measurement　of　energy　efficiency　is　the　cornerstone　of　improving　energy　efficiency　and　realizing　energy　transition.　Considering　that　the　production　technology　of　each　region　is　restrained　by　factors　including　economic　development　and　natural　resource　endowment,　this　paper　first　uses　the　emergy　theory　to　measure　the　ecological　carrying　capacity　of　each　region,　and　then　selects　other　representative　data　to　construct　the　＂Ecology-Economy-Geography＂　heterogeneous　framework.　From　the　perspective　of　energy　input　minimization,　the　spatial　and　temporal　features　of　China＇s　ecological　total　factor　energy　efficiency　(ETFEE)　from　2006　to　2019　have　been　discussed　by　employing　the　sequential　directional　SBM　model　and　Luenberger　productivity　index.　After　robustness　tests,　we　conclude　that:　(a)　The　grouping　results　under　multidimensional　variables　are　different　from　the　traditional　grouping　of　＂East-Central-West＂;　(b)　The　meta-frontier　Ecological　Total　Factor　Energy　Efficiency　(METFEE)　and　group　frontier　Ecological　Total　Factor　Energy　Efficiency　(GETFEE)　vary　in　spatial　distribution　and　temporal　change;　(c)　Technological　progress　is　the　key　to　improving　METFEE,　but　part　of　the　improvement　will　be　offset　by　diminishing　returns　of　＂catch-up　effect＂.　Finally,　policy　recommendations　to　promote　the　ecological　total　factor　energy　efficiency　in　China　are　put　forward.