The urea selective catalytic reduction (Urea—SCR) system has been widely used in the aftertreatment system of diesel engine, in which the injection quantity of urea is selected as the control input. By the precise control of the ammonia coverage rate, the poisonous NOx can be converted to the environmentally friendly N2 and H2O. As Urea—SCR system has nonlinear characteristics and disturbance is difficult to model, a two degree of freedom control system consisting of a feedforward controller and an H∞ feedback controller was developed. Firstly, the Urea—SCR system model was deduced based on the principle of chemical reaction kinetics. Secondly, the feedforward controller was designed based on the differential flatness method. The flatness output was chose as ammonia coverage rate, then the system state, control input were expressed by flatness output and its finite order derivatives, based on this, the feedforward control input was obtained. Thirdly, the Taylor expansion of the Urea—SCR system model was carried out at the equilibrium point of the feedforward control input, the un-modeling dynamics of urea and parameter uncertainties were considered as the amplitude-bounded disturbance input. The feedback control controller which satisfied the H∞ performance index was designed to accurately control the ammonia coverage rate. Finally, the tracking performance and robustness were verified by the simulation results with the engine dynamics simulation software enDYNA under FTP75 test cycle.