Based on a four-seat electric aircraft, the aerodynamic layout of the aircraft with fuel cell propulsion system was designed, and three aerodynamic layout schemes were formed respectively, including internal FC reactor and hydrogen tank scheme, internal FC reactor and external hydrogen tank scheme, external FC reactor and hydrogen tank scheme. The computational fluid dynamics software was used for numerical simulation, and the aerodynamic characteristics of the three schemes were analyzed in terms of lift and drag characteristics, longitudinal and transverse directional static stability. The analysis results show that the lift-drag characteristics of the internal reactor and hydrogen tank is the best, the cruising resistance coefficient will be increased by orders of 0.004 and 0.007 for both internal FC reactor and external hydrogen tank scheme and external FC reactor and hydrogen tank scheme respectively, the lateral static stability of the two schemes using the external layout is improved compared with that of the internal layout scheme, while the longitudinal and directional static stability changes little. Compared with the wind tunnel test results, the accuracy of the simulation results is proved. This study is beneficial to explore the aerodynamic layout design of fuel cell aircraft and has certain engineering reference value.