The selective catalytic reduction (SCR) system is a highly-effective aftertreatment device for NOx reduction of diesel engines. Generally, the ammonia ($NH_3$) was generated from reaction mechanism of SCR in the SCR system using the liquid urea as the reluctant. Therefore, the precise urea dosing control is a very important key for NOx and $NH_3$ slip reduction in the SCR system. This paper investigated NOx and $NH_3$ emission characteristics of urea-SCR dosing system based on model-based control algorithm in order to reduce NOx. In the map-based control algorithm, target amount of urea solution was determined by mass flow rate of exhaust gas obtained from engine rpm, torque and $O_2$ for feed-back control NOx concentration should be measured by NOx sensor. Moreover, this algorithm can not estimate $NH_3$ absorbed on the catalyst. Hence, the urea injection can be too rich or too lean. In this study, the model-based control algorithm was developed and evaluated on the numerical model describing physical and chemical phenomena in SCR system. One channel thermo-fluid model coupled with finely tuned chemical reaction model was applied to this control algorithm. The vehicle test was carried out by using map-based and model-based control algorithms in the NEDC mode in order to evaluate the performance of the model based control algorithm.