This paper introduces a fuel cell system model based on energetic macroscopic representation (EMR). EMR is a causal graphic modeling approach to describe complex multidomain systems, which facilitates inversion-based control structure development called maximum control structure (MCS). The EMR model is derived for a commercially available fuel cell system and corresponds well with experimental results. An inversion-based control is proposed for the air supply subsystem. The control corresponds well with the unknown internal control. The application of EMR and MCS marks a promising approach: Control structure development based on experience is replaced by a systematic approach. This is especially meaningful for complex multidomain systems such as fuel cell systems.