Piggery wastewater with high concentration of carbon and nitrogen could be effectively treated by aerobic granular sludge (AGS). However, the underlying mechanisms responsible for simultaneous nitrogen and carbon removal have not been well revealed. Here we conducted a combined analysis of microbial community, denitrification genes and mathematical model calculation to illuminate the metabolic process of this AGS. The relative abundances of the dominant microorganisms were Comamonadaceae (accounting for 24.79%, including Comamonadaceae-un, Ideonella, Comamonas and Variovorax), Saccharibacteria-un (6.07%), Ideonella (5.51%), Luteimonas (4.81%), Bacteroidales (4.09%), Niabella (3.95%), Fillimonas (3.53%), Thauera (3.51%) and Pseudoxanthomonas (3.44%). The dominant microorganisms in the AGS mainly had the potentials of heterotrophic nitrification, aerobic denitrification, organic macromolecule degradation, organics storage and granule stability maintaining. Interestingly, only 0.145% of the communities were found as autotrophic nitrifiers. Moreover, the quantitative analysis of denitrification genes showed the abundance of napA gene was significantly higher than that of narG gene, suggesting that aerobic and anoxic denitrification process coexisted in the AGS, and the former was dominant. Furthermore, the calculations based on mathematical model were used to deduce the nitrification, denitrification and organic matter utilization process in one running cycle of the AGS. The results also indicated that the rapid organic substrates storage in the feast phase might resist the impact of high strength wastewater, and provide carbon and energy sources in the famine phase. Together, our study elucidated the nitrogen and carbon removal process of the AGS treating piggery wastewater with high concentrations.