Pyrite-driven　autotrophic　denitrification　(PAD)　presents　a　promising　and　sustainable　process　for　nitrate　removal　from　aquatic　environments,　yet　its　engineering　application　has　been　constrained　by　suboptimal　denitrification　efficiency.　This　study　demonstrated　an　innovative　hydrogen-annealing　strategy　to　engineer　sulfur　vacancies　(SVs)　in　pyrite　(AH2),　achieving　breakthrough　performance　in　both　nitrogen　and　phosphorus　elimination.　The　introduction　of　SVs　into　pyrite　enhanced　nitrate　removal　activity　by　28.62　times　compared　to　the　pristine　pyrite.　In　addition,　the　removal　efficiencies　of　nitrate　and　phosphorus　in　AH2　group　maintained　over　99　%　after　112-d　operation.　Surface　structural　characterization　revealed　that　the　formation　of　SVs　weakened　the　Fe[sbnd]S　bond　strength　in　pyrite,　promoting　electron　transfer,　oxidation　rates,　and　Fe(II)/Fe(III)　cycling　within　the　AH2　system.　Microbial　community　analysis　demonstrated　that　SVs　favored　the　significant　enrichment　of　Fe(II)/sulfur-dependent　autotrophic　denitrifying　bacteria　such　as　Thiobacillus　in　AH2　system.　In　addition,　the　occurrence　of　iron-reducing　bacterium　(IRB)　such　as　Anaerolinea　promoted　Fe(II)/Fe(III)　cycling,　thus　prevented　cellular　crusting　and　ensured　long-term　stability　of　PAD　system.　Metagenomic　results　demonstrated　that　SVs　upregulated　key　functional　genes　associated　with　N-S-Fe　transformations.　This　work　elucidates　structure-activity　relationships　between　crystal　defects　and　PAD　performance,　provides　fundamental　insights　into　electron　transfer　and　N-S-Fe　transformation　in　response　to　SVs　of　pyrite,　and　proposes　vacancy　engineering　strategies　for　optimizing　pyrite-based　wastewater　treatment　process　in　future　practical　applications.　©　2025　Elsevier　B.V.