Transgenic rice cells using RAmy3D promoter can provide high productivity, and the production of recombinant protein is induced by sugar starvation. In this system, productivity was reduced during the scale-up processes. To ensure the influences of shear stress and oxygen transfer rate, working volume and mixing performances were investigated under various agitation speeds and working volumes. In addition, inoculation methods including suspended cells and filtered cells were compared. Working volumes and shaking speeds were 300, 450 mL and 80, 120 rpm, respectively. Hydrodynamic environment of each condition was measured numerically like mixing time and k L a. Good mixing performance and high shear stress were measured at high agitation speed and low volume. The highest level of hCTLA4Ig was 30.7 mg/L at 120 rpm, 300 mL. When conditioned medium was used for inoculation, increased cell growth was noticed during the day 0~4 and decreased slower than filtered cells. Compared with filtered cells, the maximum hCTLA4Ig level reached 37.8 mg/L at 120 rpm, 300 mL and lower protease activity level was observed. In conclusion mixing performance is critical factor for productivity and conditioned medium can have a positive effect on damaged cells caused by hydrodynamic shear stress.