In response to the growing challenges of nitrogen oxides (NOX) emission control, NH3-based selective catalytic reduction (SCR) technology has been widely adopted to reduce NOX emission from marine diesel engine exhaust. In this study, the SCR mechanism model is based on a refined eight-state model. A novel structure of SCR-DeNOX system is established, which incorporates a by-pass valve and pipe. Unlike existing parallel and series SCR-DeNOX platforms, the novel structure shows a certain advantage in reducing NH3 and maintains a relatively high NOX conversion efficiency. Adaptive sliding mode observers (ASMO) are designed to generate dynamic ammonia coverage ratio references, replacing traditional fixed references. In addition, they also address the variations in the SCR-DeNOX model. The sliding mode control (SMC) is used to track the ammonia coverage ratio reference in upper cell by controlling ammonia injection. The decoupling with SMC (DC-SMC) is proposed to track the ammonia coverage ratio reference in the lower cell by controlling split ratio. The simulation results show the system with DC-SMC shows a 15.46% improvement in NOX conversion efficiency compared to that with SMC. Additionally, it shows a lower NH3 cost.