Mobile machinery means a power-driven vehicle that is specifically designed and constructed to perform work on or off the road. To reduce the nitrogen oxide (NOx) emissions that come from mobile machinery, a combination of a physical model and closed-loop control is applied to the selective catalytic reduction (SCR) system. Based on the design of the variable cross-section extended exhaust structure, the differential pressure measurement was achieved, and the physical model of the exhaust flow based on the differential pressure was established. Based on the analysis of the heat and mass transfer process of the SCR catalyst, a prediction model for the internal temperature field of the catalyst was established by combining the upstream and downstream exhaust temperature sensors. Using the SCR downstream nitrogen oxides signal and the proportional–integral–derivative (PID) closed-loop control algorithm, segmented PID closed-loop control under the large hysteresis response of the SCR system was realized. The above algorithms were used to form the control code through MATLAB/Simulink and downloaded to the embedded microprocessor. The test results show that the established model can realize the real-time calculation of the exhaust gas flow rate and the internal temperature of the catalyst. Under steady-state conditions, the calculation error of the exhaust flow rate is less than ±3%, and the calculation error of the catalyst temperature is less than ±5%. Under transient conditions, the calculation error of the exhaust flow rate is less than ±9%, and the calculation error of the catalyst temperature is less than ±8%. The nitrogen–oxygen signal-based PID closed-loop algorithm can improve the nitrogen–oxygen conversion efficiency and control accuracy of the model.