The targeted purpose here is the control of a nonlinear and non-square system with three inputs and two outputs in order to reduce soot and greenhouse gas pollutants. In this paper, a non-square multivariable controller for the air-path system of a turbocharged Diesel engine is proposed. The controller is designed using the CRONE (Commande Robuste d'Ordre Non Entier) Control-System-Design approach to maintain performance and robust stability for a wide set of operating points. In this research, we focused on the multi-input multi-output system identification problem, and test-bench data were processed to find a nominal linear model. The controller was then designed via an open-loop transfer function optimization. Finally, simulation results from a simulation model show the performance of the proposed control-system.