Water System is an important system in civil aircraft. During the design of water system, the design of pipe is a key part. And the numerical simulation of pipe flow can help the design and optimization of pipe. So in this paper, the study on numerical simulation of supply pipe flow in civil aircraft water system is presented, for better use of the numerical simulation in the design of water system pipe. Under different conditions of pressure drops and wall roughness, the water supply pipe flow is simulated with FLOWMASTER Pipe Network System and CFD, and the results of the two methods are analysed . Comparing the simulation of the two methods shows that FLOWMASTER Pipe Network System can obtain the main performance of pipe rapidly, accurately and reliably, such as flow rate; and CFD can get detail information of pipe flow field. In the design of water system pipe, the two methods should be used in conjunction, playing their respective advantages, to finish the work better with the help of complementary advantages of the two methods.