In this paper, we propose a Control Lyapunov Function based nonlinear robust controller for turbocharged Diesel engine. The basic idea is to develop inverse optimal control and utilize more general Lyapunov function which provides additional degree of freedom in order to achieve better performance. The obtained controller gain guarantees the global convergence of the Diesel engine system and regulates the flows for the Variable Geometry Turbocharger and Exhaust Gas Recirculation systems in order to optimize oxygen-fuel ratio and intake manifold EGR fraction. Simulation of the control performance based on professional simulator AMESim (LMS) shows the effectiveness of this approach.