Using an electric propulsion system instead of internal combustion engine power, electric aircraft have the advantages of energy conservation and environmental protection. This paper proposed an analysis method of the water cooling system for the frequency converter of an electric aircraft which aims at increasing the power density of the frequency converter. The turbulence of the cooling water influence heat dissipation, which is important in the calculation of fluent field. Based on fluent field calculation, the relationships between the flow quantity and temperature, the flow quantity and pressure, the flow velocity and temperature, and the flow velocity and pressure of the water cooling system are received, which guided the design of the water cooling system. Then the flow quantity is determined to be 0.8m3/h, the cross-section of the cooling water channel is determined to be 9.5mm×10mm, and the maximum temperature of the converter frequency is 67.27°C, which is verified by the experiment. The calculation results for the final water cooling system are within usage requirements which benefit future design.