Abstract: Disclosed are a system and method for efficient nitrogen and carbon removal and phosphorus recovery of source-separated fresh urine by biochemical combination. The system includes a functionally zoned membrane aerated biofilm reactor for in-situ nitrogen and carbon removal, a source separation toilet, a source-separated urine storage tank, a phosphorus recovery reactor, a calcium salt solution tank, a water production tank, and a control system. The membrane aerated biofilm reactor is divided into an upper part and a lower part, a micro-aerobic environment is formed in the upper part while an anaerobic environment is formed in the lower part, and thus nitrogen and carbon can be removed only in the membrane aerated biofilm reactor. The system disclosed by the present disclosure can achieve the goal of removing nitrogen and carbon by 95% and more without additional carbon source, and can meet the demand of in-situ sewage treatment on a train.