In this work, we investigate the cycle-based optimal emission control for Diesel engine selective catalyst reduction (SCR) systems. Considering the main chemical reactions inside a SCR cell, a three-state nonlinear model is obtained and the system parameters are determined by using the experimental data. Though there are considerable works on the SCR dosage control in the literature, the optimal control strategy applied to the SCR systems has been rarely studied. The global optimality in the SCR dosage control can be used as a benchmark and evaluate the performance of other designed controllers. Moreover, it can be employed to find the limit of NOx conversion efficiency of a specific SCR aftertreatment system. Therefore, it is quite meaningful to study the optimal emission control of SCR systems via the dynamic programming approach. Due to the system stiffness and the huge computational load, we propose the dynamic programming algorithm based on the continuous-time SCR model. The proposed algorithm is applied to the SCR system and the verification is carried out based on the US06 test cycle. The prescribed ammonia slip constraint is satisfied and the tailpipe NOx emission is optimized.