From the perspective of mass flow, the conventional municipal wastewater treatment based on active sludge process (CAS) removes pollutants by aerobically converting organic carbon (C) into useless CO2 with excess sludge as a by-product and removing nitrogen (N) in the form of N-2 by nitrification/denitrification with aeration energy and the carbon source input. To improve sustainability, in this paper, we propose a novel process based on the coagulation adsorption enhanced membrane (CAEM) method, which redesigns the C and N mass flows for energy-neutral wastewater treatment. A pilot-scale operation conducted over two months demonstrated that up to 85.6% chemical oxygen demand (COD) was rejected by CAEM, which could be directed into the anaerobic energy recovery unit in a concentrated form with high biodegradability. Meanwhile, 74.9% nitrogen was kept in the mainstream for the subsequent autotrophic deammonification. Modelling results based on steady-state mass balance and stoichiometric calculations indicated the changes in the C and N mass flows induced by CAEM. The amount of organics (COD) used for energy production increased remarkably compared with that in the CAS process. Combined with mainstream deammonification, this CAEM-based process also avoided the COD consumed by denitrification and heterotrophic oxidation, leading to less aeration and energy consumption (0.22 kWh/t in the CAS process vs. 0.05 kWh/t in the CAEM-based process). The proposed CAEM-based process redesigned a larger C mass flow to the anaerobic energy recovery unit than energy-intensive aerobic oxidation and more N removal by autotrophic deammonification than by heterotrophic deammonification, making it feasible to achieve energy neutrality.