In this paper, a novel control solution is proposed and validated, for the decoupling control of variable geometry turbine (VGT) and exhaust gas recirculation (EGR) system in diesel engines. The cross-coupling and dynamics variation are lumped together as total disturbance, estimated and cancelled in real time by active disturbance rejection control (ADRC). The static and dynamic feed-forward controllers were added to further enhance the disturbance rejection. This proposed solution is compared with the existing PID solution in simulation based on a well-established model, demonstrating its superiority in response speed, robustness, and simplicity in parameters tuning.