Dual-loop exhaust gas recirculation (EGR) with variable geometry turbocharger (VGT) is an effective technique to simultaneously control intake manifold conditions (pressure, temperature, and burned gas mass fraction) in Diesel engines. To address the control problem for this highly coupled and complicatedly dynamic multi-input multi-output (MIMO) system, this paper proposed a control method with decoupled-feedforward loop. Through investigating the dynamics of airpath loop system, a linear-quadratic regulator (LQR) with a decoupled-feedforward control strategy was utilized for the control of the intake manifold conditions. The proposed method was validated and compared with the conventional LQR method via a high-fidelity GT-Power model.