Evidence shows physical environment and mechanical stress plays a crucial role in stem cell modulation in vitro. For example, it has been reported that stem cell in normal gravitational condition is spread with a spindle configuration, while in the simulated microgravity conditions it transforms to a rounded non-spread shape. In this paper a computational simulation approach is used to evaluate the impact of microgravity on mechanical behavior of stem cells under flow-induced shear stresses. Using computational fluid dynamics and fluid structure interactions methods, the influence of a well-defined flow passing over a single stem cell was simulated in two different gravitational conditions. The simulation was performed using Arbitrary Lagrangian-Eulerian (ALE) formulation and adaptive mesh procedure using a 3D model of a stem cell discretized via finite element method. The results suggest the significant change in the distribution of the stresses and strains inside the cytoplasmic region in the microgravity condition. This may be explained by the disruption of the cytoskeletal fibers and resulting effects on cell biological functions. Focusing on fluid-structure interactions (FSI), we developed a cell-scale model for investigation of the mechanical behavior of the stem cells. Our results comprise the changes in mechanotransduction mechanisms because of microgravity which in turn affect the stem cell lineage commitment.