As an important secondary power source of the aircraft, the control performance of the Auxiliary Power Unit (APU) will directly affect the working efficiency of the aero-engines and the aircraft systems. However, APU has complex nonlinear characteristics and faces the influence of various inevitable and uncertain disturbances. Therefore, the design of its high-performance control system is extremely challenging, and the traditional gain-scheduling PI control method cannot meet this demand. To resolve this problem, we design an Active Disturbance Rejection Control (ADRC) scheme for APU systems. At the same time, the parametric design method of the proposed ADRC is given, so that the corresponding control parameters can be set according to the linearized model in engineering applications. Finally, a numerical comparison simulation is carried out on a certain auxiliary power unit model to verify the effectiveness and superiority of the proposed method.