The structure of a bone tissue is capable of adapting to mechanical loading through the process of bone remodeling, which is regulated by osteoblasts and osteoclasts. Fluid flow within trabecular porosity under cyclic loading is one of the factors stimulating the biological response of osteoblasts and osteoclasts. However, the relation between loading directions and interstitial fluid flow was seldom studied. In the present study, a finite element model based on micro-computed tomographic reconstructions is built by using a mouse femur. Results from the fluid–solid coupling numerical simulation indicate that the loading in different directions generates a distinct distribution of von Mises stress in the bone matrix and a fluid shear stress (FSS) in the bone marrow. The loading along the physiological direction leads to a more uniform distribution of solid stress and produces an FSS level beneficial to the biological response of osteoblasts and osteoclasts compared with those along the non-physiological direction. There was a minimum threshold line of wall FSS with a specific solid stress at the bone surface, suggesting that the wall FSS is mainly induced by the solid strain. These results may offer fundamental data in understanding the mechanical environment around osteoblasts and osteoclasts and the cellular and molecular mechanisms of mechanical loading-induced bone remodeling.