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The sequencing batch reactor (SBR) has been increasingly applied in the control of high organic wastewater. In this study, SBR with aerobic granular sludge was used for wastewater treatment in a noodle-manufacturing village in Vietnam. The results showed that after two months of operation, the chemical oxygen demand, total nitrogen and total phosphorous removal efficiency of aerobic granular SBR reached 92%, 83% and 75%, respectively. Bacterial diversity and bacterial community in wastewater treatment were examined using Illumina Miseq sequencing to amplify the V3-V4 regions of the 16S rRNA gene. A high diversity of bacteria was observed in the activated sludge, with more than 400 bacterial genera and 700 species. The predominant genus was Lactococcus (21.35%) mainly containing Lactococcus chungangensis species. Predicted functional analysis showed a high representation of genes involved in membrane transport (12.217%), amino acid metabolism (10.067%), and carbohydrate metabolism (9.597%). Genes responsible for starch and sucrose metabolism accounted for 0.57% of the total reads and the composition of starch hydrolytic enzymes including α-amylase, starch phosphorylase, glucoamylase, pullulanase, α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, and 1,4-α-glucan branching enzyme. The presence of these enzymes in the SBR system may improve the removal of starch pollutants in wastewater.