In this paper, a nonlinear active disturbance rejection control (NLADRC) strategy based on nonlinear extended state observer (NLESO) is proposed to solve the unmodeled dynamics, coupling and disturbance due to change of working point in the variable geometry turbine (VGT) and exhaust gas recirculation (EGR) system, so as to achieve accurate control of intake manifold pressure and mass air flow in a diesel engine. To achieve decoupling, the double-input double-output (DIDO) VGT-EGR system is decomposed into two single-input single-output (SISO) subsystems, and each subsystem has a separate nonlinear active disturbance rejection controller. At the same time, the convergence proof of the designed NLESO is also given theoretically. Finally, the NLADRC controller is compared with linear active disturbance rejection controller and proportional–integral–derivative (PID) controller. Through simulation, it is indicated that the proposed NLADRC controller has better transient response performance, resistance to external disturbance and robustness to the change of engine operating point.