Shortcut nitrification-denitrification, anaerobic ammonium oxidation (ANAMMOX), and methanogenesis have been successfully coupled in an Expanded Granular Sludge Bed-Biological Aerated Filter (EGSB-BAF) integrated system. As fed different synthetic wastewater with chemical oxygen demand (COD) of 300–1200 mg·L and of 30–120 mg·L at the outer recycle ratio of 200%, the influence of influent on ANAMMOX in the integrated system was investigated in this paper. The experimental results showed that higher COD concentration caused an increase in denitrification and methanogenesis but a decrease in ANAMMOX; however, when an influent with the low concentration of COD was used, the opposite changes could be observed. Higher influent concentration favored ANAMMOX when the COD concentration of influent was fixed. Therefore, low ratio would decrease competition for nitrite between ANAMMOX and denitrification, which was favorable for reducing the negative effect of organic COD on ANAMMOX. The good performance of the integrated system indicated that the bacterial community of denitrification, ANAMMOX, and methanogenesis could be dynamically maintained in the sludge of EGSB reactor for a certain range of influent.