Fuel cell powered unmanned aerial vehicle （UAV） is an important technical path to achieve green and low-carbon aviation. With the development of UAV to large scale and long range， the thermal management problem of high-power fuel cell under the complex flight profile of UAV becomes more complicated. This paper presents a heat exchanger design based on ducted propeller structure， which makes full use of the airflow behind the propeller to dissipate heat without adding too much system mass. At the same time， a fuel cell thermal management system scheme for UAV is proposed based on the ducted propeller heat exchanger. The simulation model of the thermal management system is established by using the Amesim platform combined with the typical UAV flight profile， and the numerical simulation research is carried out. The results show that： （1） the thermal management system can better control the temperature of the fuel cell. The inlet coolant temperature does not exceed 61.3 ℃ （target value： 60 ℃）， and the inlet-outlet coolant temperature difference does not exceed 11.1 ℃ （target value： 10 ℃）， both of which remain within the allowable error tolerance，and verify the feasibility of the ducted propeller heat exchanger scheme； （2） When the total number of ducted propeller heat exchangers is the same， the number of heat exchangers of each heat exchanger module should be designed to match the power of each stage of the fuel cell and the flow characteristics of the electric pump.