A pilot-scale internal circulation-anoxic/oxic (IC-A/O) coupling reactor was performed for soybean protein wastewater treatment. Results indicated that after the IC-A/O coupling system, the CODcr (8000-10,000 mg.L-1) and NH3-N (250-270 mg.L-1, decomposed from the organic nitrogen) in influent of soybean protein wastewater was greatly reduced to 70-90 mg.L-1 and < 4 mg.L-1, respectively, which indicated a successful start-up of ICA/O coupling system. The hydraulic retention time (HRT) of the IC reactor kept being 24 h with CODcr removal constant at 90% (pH of the reactor at 7.0-7.4). The inflow, NH3-N and CODcr volume loadings in the A/O system also affect the performance of the IC-A/O coupling system. The macrograph SEM indicated the spheroidicity-shaped anaerobic granular sludge (with diameter of 1-2 mm) in IC reactor, which mainly composed of large amounts of bacilli microorganisms playing a skeletal role in the sludge formation, with wrapped some cocci microorganisms; this also corresponded well with the analysis of bacterial community structure. SEM images of sludge morphology indicated that bacillus microorganisms played a predominant role on the microbial morphology of granular sludge not only in anoxic system, but also in oxic system. This result was proven by the overlap of OUT_1664 in Venn figure.