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This paper presents a diesel engine selective catalytic reduction (SCR) ammonia surface coverage ratio profile control design for a two-cell SCR system, which enables a staircase ammonia coverage ratio profile for simultaneously achieving high NOx conversion efficiency and low ammonia slip. Such a novel two-cell SCR architecture greatly increases the control system complexity. A nonlinear backstepping-based control law is proposed to regulate the ammonia coverage ratio of the upstream cell to a desired (high) value in order to maintain high-SCR NOx conversion efficiency, and to keep the ammonia coverage ratio of the downstream cell below a low upper limit for high-ammonia adsorption capability. The control law thus possesses the advantages of being able to simultaneously maintain SCR high-NOx conversion efficiency and guarantee low ammonia slip, as well as being robust to the SCR ammonia storage capacity uncertainty. Theoretical analyses and FTP75 driving cycle simulations based on an experimentally validated full-vehicle simulator were conducted to evaluate the effectiveness of the proposed control strategy. Comparisons with conventional SCR controllers are presented to show the advantages of the proposed two-cell backstepping-based SCR control strategy.