The diesel Auxiliary Power Unit (APU) for vehicle applications is a complex nonlinear system. For the purpose of this paper presents a dynamic average model of the whole system in an entirely physical way, which accounts for the non-ideal behavior of the diode rectifier, the nonlinear phenomena of generator-rectifier set in an elegant way, and also the dynamics of the dc load and diesel engine. Simulation results show the accuracy of the model. Based on the average model, a simple PI control scheme is proposed for the multivariable system, which includes the steps of model linearization, separate PI controller design with robust tuning rules, stability verification of the overall system by considering it as an uncertain one. Finally it is tested on a detailed switching model and good performances are shown for both set-point following and disturbance rejection.