This paper focuses on the virtual integration and test approach used for the evaluation of an automation system developed for the multifunctional operation of fuel cells in commercial aircraft. In order to accomplish the virtual integration a model of the overall automation system is linked with a dynamic model of the complete fuel cell system. For this purpose a modeling approach for complex physical systems is described in this paper. During virtual testing various simulation runs are executed based on automatically generated test cases, which cover a complete flight mission. For this reason a flight mission is modeled as a Statechart that includes next to time- based flight phases also potential events and malfunctions (e.g. engine flame-out, cargo fire). An algorithm is described, which can find all possible state combinations including parallel event sequences. Afterwards test cases are automatically generated using segmented flight profiles in order to integrate atmospheric pressure and temperature as well as airspeed. During each simulation run so-called evaluation agents analyze and compare certain operational states with corresponding specifications. The global results are visualized using three-dimensional plots. The presented approach is illustrated in this paper using a simple example of a fuel cell system that operates multiple functions during a flight mission.