The wastewater system is an important aircraft part of civil aircraft. The effective sewage discharge is closely related to the ride comfort and health of passengers. In this work, Euler method was used to simulate the gas-liquid solid three-phase flow in wastewater system, and the effect of flight height and working condition of toilet on wastewater emission has been analyzed. Results show that: when only the farthest toilet works, with the increase of flight altitude, the core peak time of waste water flow is brought forward, and the time required for waste water to be completely discharged are significantly shortened from 3.31s to 1.87s, and the waste water can be quickly discharged into the waste water tank. When the three toilets work at the same time, the negative pressure in the waste water pipeline will be reduced, and the flow rate of different cross sections will decrease by 66.5% on average, the toilet close to the waste water tank will reduce the discharge efficiency of the farthest toilet, resulting in the waste water cannot be discharged quickly. When the flushing time of toilet close to wastewater tank is adjusted to 2s, and the farthest toilet needs to be opened separately, the wastewater in the farthest toilet can be fully discharged into the wastewater tank.