To effectively treat actual ammonia-rich CMR from resource utilization wastewater, we optimized an anaerobic-microaerobic two-stage expanded granular sludge bed (EGSB) and moving bed sequencing batch reactor (MBSBR) combined system. By controlling dissolved oxygen (DO) levels, impressive removal efficiencies were achieved. Microaeration, contrasting with anaerobic conditions, bolstered dehydrogenase activity and electron transfer, thereby augmenting the functional microorganism community. The heightened relative abundance of Synergistetes and Proteobacteria facilitated hydrolytic acidification, fostering nitrogen and phosphorus removal. Furthermore, we examined the impact of DO concentration in MBSBR on pollutant removal and microbial metabolic activity, pinpointing 2.5 mg/L as the optimal DO concentration for superior removal performance and energy conservation.