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Grooved channel bioreactors have shown great applications in cell biology studies by creating a controlled cellular microenvironment and protecting it from destructive influences of fluidic shear stress. Despite numerous studies on improvement in cell docking and retention in microchannels, the lack of reliable criteria for determining optimal groove geometries seems to be a great barrier in the field. In this study, a systematic approach was used to find the critical geometrical parameters that yield to the highest cell shear protection against the upstream flow. To achieve this goal, the lattice Boltzmann method was used to simulate the flow inside a grooved microchannel due to its incredible reliability for portraying complex streamlines in microflow phenomenon. The simulation results showed that the flow behavior within microgrooves considerably varies with groove/channel geometry and that based on the generated microcirculation regions, there are correlations between groove/channel width, depth and the maximum shear protection factor, which led toward finding reliable criteria for optimization of such parameters. The results could be beneficial for researchers to design such devices based on different cell sizes, cell behavior and geometrical constraints while ensuring protected cell culture environment.