In high-altitude environment, the PEMFC UAV face challenges such as insufficient oxygen supply and reduced power output, which seriously affects the performance and range of the UAV. In order to improve the system output performance, this paper proposes a net power optimization method for high-altitude PEMFC system based on pressure ratio and model predictive control. Firstly, a model of the air supply system applicable to variable altitude conditions is established, and then the analysis of the operating characteristics of the air compressor and the surge line is carried out. Secondly, considering the effect of pressure ratio on the power of stack and air compressor, a net power optimisation scheme based on pressure ratio is designed to obtain the best operating trajectory. Then, a pressure ratio control method based on model predictive control is proposed to realize the tracking of the optimal working point. Finally, the comparative experiments on the air supply system test platform show that the proposed strategy can effectively improve the net power of the PEMFC system under variable altitude conditions.