Fluid shear stress (FSS) caused by interstitial fluid flow within trabecular bone cavities under mechanical loading is the key factor of stimulating biological response of bone cells. Therefore, to investigate the FSS distribution within cancellous bone is important for understanding the transduction process of mechanical forces within alveolar bone and the regulatory mechanism at cell level during tooth development and orthodontics. In the present study, the orthodontic tooth movement experiment on rats was first performed. Finite element model of tooth-periodontal ligament-alveolar bone based on micro computed tomography (micro-CT) images was established and the strain field in alveolar bone was analyzed. An ideal model was constructed mimicking the porous structure of actual rat alveolar bone. Fluid flow in bone was predicted by using fluid-solid coupling numerical simulation. Dynamic occlusal loading with orthodontic tension loading or compression loading was applied on the ideal model. The results showed that FSS on the surface of the trabeculae along occlusal direction was higher than that along perpendicular to occlusal direction, and orthodontic force has little effect on FSS within alveolar bone. This study suggests that the orientation of occlusal loading can be changed clinically by adjusting the shape of occlusal surface, then FSS with different level could be produced on trabecular surface, which further activates the biological response of bone cells and finally regulates the remodeling of alveolar bone.