In the high-altitude environment, the thin oxygen and low atmospheric pressure not only diminish the net power of the proton exchange membrane fuel cell (PEMFC) system but also intensify the complexity of safe and stable operation. In this article, a performance guaranteed control strategy (PGCS) for high altitude is proposed, which can deal with optimal trajectory search and cooperative control of the system under the aggravation of multivariable coupling caused by environmental changes. Based on the close energy interaction between the system and environment, the PEMFC system model for high altitude is established. Considering the characteristics of atmospheric environment changing with altitude and the harm of surge and choke to the system, the safe constraints of the system are obtained. The optimization based on variable coupling partial derivative constraint is proposed to realize the net power optimal trajectory search. A cooperative sliding mode control is proposed to realize the optimal trajectory tracking of the multiple input multiple output system. The comparative experiments on the hardware-in-the-loop platform show that the proposed PGCS can effectively improve the net power, maintain safe, and stable operation of the PEMFC system for high altitude.