To　explore　the　effects　of　wastewater　feeding　modes　on　the　formation　of　aerobic　granular　sludge　(AGS)　and　the　complex　relationships　between　resistance　genes　and　bacteria,　two　pilot-scale　sequencing　batch　reactors　(SBRs)　were　established.　The　SBR　with　influent　wastewater　introduced　uniformly　through　pipes　at　bottom　was　designated　as　BSBR,　and　the　SBR　with　inlet　wastewater　flowing　directly　from　top　was　TSBR.　BSBR　formed　dense　AGS　due　to　uniform　wastewater　feeding　at　bottom,　while　TSBR　failed　to　cultivate　AGS.　Metagenomic　sequencing　illustrated　that　rapid　growth　of　AGS　in　BSBR　was　accompanied　with　increase　of　antibiotic　resistance　genes　(ARGs)　abundance,　but　ARGs　diminished　when　the　size　of　AGS　was　stable.　The　ARGs　continued　to　elevate　in　TSBR,　and　abundance　of　metal　resistance　genes　(MRGs)　was　always　higher　than　that　in　BSBR.　Two　reactors　had　markedly　different　bacterial　community,　microbes　in　BSBR　owned　stronger　activity,　conferred　greater　potential　to　proliferate.　AdeF　in　two　systems　had　the　most　complex　gene-bacteria　relationships　which　would　undergo　HGT　within　bacterial　genus.　The　different　feeding　modes　of　wastewater　directly　led　to　the　changing　size　of　sludge,　which　caused　knock-on　effects　of　variations　in　the　abundance　of　microbial　communities　and　resistance　genes.　This　study　provided　promising　suggestions　for　the　rapid　cultivation　of　AGS　and　control　of　resistance　genes　at　pilot-scale.