Urea-based selected catalytic reduction (SCR) systems are effective ways in diesel engine after-treatment systems to meet increasingly stringent emission regulations. To achieve high NOx reduction efficiency and low NH3 slip, the control of the SCR system becomes more challenging, especially in transient operating conditions with model uncertainties. To effectively address this issue, this paper proposed a compound control strategy with a switching mechanism between an active disturbance rejection (ADR) controller and a zero-input controller. The ADR controller estimates and rejects the total (internal and external) disturbances from the SCR system when the exhaust gas temperature is high and its variation is small. The zero-input controller is used to lower ammonia surface coverage ratio to avoid high ammonia slip when exhaust gas temperature suddenly rises. The proposed control strategy is validated through a high-fidelity GT-Power simulation for a light-duty diesel engine over steady states and federal test procedure (FTP-75) test cycle. Its effectiveness is demonstrated especially in rapidly transient conditions with model uncertainties.