The partial nitritation-anammox process based on a membrane-aerated biofilm reactor (MABR) faces several challenges, such as difficulty in suppressing nitrite-oxidizing bacteria (NOB), excessive effluent nitrate, and ineffective synergy between denitrification and anammox bacteria. Therefore, a novel partitioned granular sludge coupling with MABR (G-MABR) was constructed. The chemical oxygen demand (COD) and nitrogen removal efficiency were 88.8 ± 1.8 %–92.6 ± 1.2 % and 88.8 ± 1.5 %–93.6 ± 0.7 %, respectively. The COD was mainly lowered in the lower granular sludge-zone, while nitrogen was removed in the upper MABR-zone. NOB was significantly suppressed in the MABR-zone due to competition for substrate with denitrifying bacteria and anammox bacteria. This partitioned configuration reduced the C/N ratio in the MABR-zone, thus facilitating autotrophic nitrogen removal. Both partial nitrification and denitrification provided nitrite for anammox bacteria in granular sludge, whereas partial nitrification mainly supplied nitrite to the anammox bacteria in membrane biofilms.