In this research, a new transient mathematical model based upon tanks-in-series configuration was developed to simulate the direct synthesis of dimethyl ether (DME) from syngas in a commercial-scale slurry bubble column reactor. A comparison between the simulation results and experimental data showed that the applied model might acceptably describe the behavior of the slurry reactor. Furthermore, simulation results in the heterogeneous bubble flow regime indicated that the proposed model with 10 tanks-in-series provided the optimum condition. Utilizing this transient model and considering catalyst deactivation, the effect of operating conditions on DME productivity and CO conversion were investigated. In addition, the dynamic behavior of the reactor was studied after implementing a step change in the reactor's coolant fluid temperature.