Research on induced Pluripotent Stem (iPS) cell has attracted attention due to their remarkable progress in regenerative medicine. Cost and quality are two main factors to be considered when using iPS cells in biological applications in a large scale. In this study, the suspension culture of iPS cells was numerically simulated in a cylindrical tank under the two-different shaking methods; one-direction rotation and periodic alternate rotation. The two shaking methods exhibited a significant difference in the average number of cells accumulated in the bottom. Even though the one direction rotation method suppressed the shear stress acting on iPS cells, after eight seconds it accumulated more cells in the bottom than the periodic alternate rotation method.