Investigating the mechanical stimuli on stem cells under in vitro and in vivo conditions is a very important topic to achieve an ability to control the cellular responses like growth, proliferation and differentiation. Many investigations carried out about biomechanical factors involved in this phenomenon and nowadays, it is proved that some factors like as cell morphology, subcellular elements configuration, scaffold architecture, substrate stiffness and mechanical stimulation via substrate displacement or fluid flow, have got an important effect on cellular responses.In this study, we have tried to evaluate the responses of a stem cell to the stiffness and thickness of the substrate by the means of finite element method. For this purpose, we have used collagen-based scaffolds as the artificial ECM and a cell culture in a bioreactor with fluid flow was simulated.by use of fluid-structure interaction method and solving the equations in two-way coupling scheme, the results show that the increase in thickness and stiffness of the substrate will result in 15 percent change in cell-substrate stresses, respectively. Also, it was seen that the change of substrate stiffness only in the range of 0.1-100 KPa could affect the cell response to an external stimulation. These results, along with other similar investigations, could be used as an instructor by the researchers to optimize the stem cell’s microenvironment in vitro, and finally get the most out of their stem cell related Investigations.