This paper describes a linear optimal control approach for advanced diesel engines equipped with complex air-path systems including a dual-loop exhaust gas recirculation (EGR) and a two-stage turbocharger. Such complex air-path systems are instrumental to achieve smooth and stable transient operation of diesel engines running advanced multiple combustion modes such as low temperature diffusion combustion (LTDC) and homogeneous charge compression ignition (HCCI). A mean-value engine model was developed to capture the main dynamics of the advanced air-path system. A linear quadratic regulator (LQR) optimal controller was designed based on a linearized model at a fixed operating point. Simulation results using a high-fidelity detailed GT-Power engine model show the effectiveness of the controller.