In this study, the heat flow of the plant scale aluminum extrusion process was investigated to establish optimum continuous heat treatment conditions. During the extrusion of 6061 aluminum alloy, processing parameters such as the extrusion pressure, speed and temperature histories of billets were logged as a function of time. The surface temperature of the billets increased at constant ram speed, while it decreased with decreases of the ram speed. In order to maintain the billet temperature within a solutionizing temperature range prior to the succeeding water quenching step, the ram speed or the temperature of the blower should be controlled. The temperature histories of the billets during the extrusion and hot air blowing processes were successfully simulated by using the velocity boundary model in ANSYS CFX. The methodology to design an optimum process by using a commercial simulation program is described in this study on the basis of the metallurgical validation results of the microstructural observation of the extrudates. The developed model allowed the advantages of taking into account the motion of the extrudate coupled with the temperature change based on empirical data. Calculations were made for the extrudate passing through the isothermal chamber maintained at appropriate temperature. It was confirmed that the continuous heat treatment system is beneficial to the productivity enhancement of the commercial aluminum extrusion industry.