The regulation of NOx emission from a diesel engine is becoming stricter by the environmental agency and furthermore, EGR has been adopted to reduce NOx emission. Air flow control of a diesel engine combined with turbocharger and EGR is complicated because turbocharger and EGR are coupled physically. This paper examines the design of a model based control structure for diesel engine with a turbocharger and EGR. Model based control provides desirable control strategies from the physical analysis of an engine model. Air fraction and exhaust manifold pressure target based control simulation was conducted in this research. Engine is highly nonlinear and susceptible to uncertainties. To overcome this problem, a robust controller was designed by using a sliding mode control method.