It　is　important　but　still　challenging　to　reveal　the　effect　of　precise　structural　modification　of　polyoxometalates　(POMs)　on　electrocatalytic　hydrogen　evolution　reaction　(HER).　Here,　we　present　the　syntheses　of　five　polyoxoniobate　(PONb)　analogs　with　well-defined　structures,　including　Na-GeNb　12　,　Cu-GeNb　12　,　GeV　2　Nb　12　,　V　3　Nb　12　,　and　SiV　2　Nb　12　,　as　model　systems,　enabling　us　to　unravel　the　effects　of　structural　modification　of　POMs　on　the　electrocatalytic　HER　at　the　atomic　level.　Our　results　revealed　that　the　bridging　O　atoms　of　PONbs　were　the　primary　active　sites　for　HER,　whose　catalytic　performance　was　mostly　affected　by　the　central　atom　of　PONb,　followed　by　surface　composition　and　then　by　counterion.　Comprehensive　characterizations　and　theoretical　calculations　were　performed　to　confirm　and　interpret　the　above　findings,　which　provide　a　rational　atomic-level　design　of　efficient　POM-based　HER　electrocatalysts.