Integrated anammox process has competitive advantages of low energy and carbon consumption in nitrogen removal. Because of the coupling of partial nitrification and anammox process, complex physicochemical and biological interactions occur in integrated anammox reactors, and long-term operation might change the characteristics which is seldom reported in previous studies. In this study, an activated sludge bioreactor and a moving bed biofilm reactor (MBBR) reactor using integrated anammox process were investigated over 450 days and compared from the startup to stable operation period. The results showed that after long-term operation, the flocs in the sludge system firstly gathered to form biofilm, and the biofilm would further form granular sludge after being manually scrapped and detached. The average ammonia removal rate (ARR) and total nitrogen removal rate (TNRR) in the transformed granular sludge system were 98.4% and 82.3%, respectively. In the MBBR reactor, because of the mass transfer resistance, the ARR and TNRR were constrained by aeration, with average values of 87.5% and 74.2% respectively, and it would be difficult to inhibit Nitrite Oxidizing Bacteria (NOB) after long-term operation due to the protection of biofilm. The biofilm and granular sludge samples in the reactors were analyzed by high-throughput sequencing of 16S rDNA amplicon, and the results revealed that the abundance of ammonia oxidation bacteria (AOB), NOB and anaerobic ammonia oxidation bacteria (AnAOB) in the biofilm was 5.66%, 2.99% and 21.10%, respectively, while the three functional bacteria in granular sludge was 7.62%, 0.34% and 6.85%, respectively. This study provides an in-depth understanding the mechanism of anammox process and broaden the feasibility of its application.