Objective To explore the effects of disuse-induced architectural changes in the osteocytic lacunar-canalicular system (LCS) on the fluid dynamic microenvironment of osteocytes under mechanical stimulus. Methods First, taking the axially loaded mice tibia as the object, a multi-scale model of ‘whole bone-single osteocyte LCS’ was established. Subsequently, pressure gradients and other results obtained from the whole-bone poroelastic finite element model were used as boundary conditions for the single-osteocyte LCS model to calculate the flow velocity and shear stress around osteocytes. Finally, a design of experiment (DOE) method was used to determine the individual and interactive effects of the LCS architectural parameters (lacunar volume, lacunar shape, and canalicular diameter) on the osteocytic fluid dynamic microenvironment within the LCS. Results When the lacunar volume, lacunar shape, and canalicular diameter changed from normal to disused, the flow velocity increased by 5.3%, 39.3%, and 37.0%, respectively. The DOE results showed that the lacunar shape and canalicular diameter had a significant effect on fluid velocity and shear stress (P<0.05), with a contribution ratio of 0.38︰0.62, whereas the lacunar volume and interaction of architectural parameters had no significant effects. Conclusions Disuse-induced changes in canalicular diameter and lacunar shape were the main factors affecting the osteocytic fluid dynamic environment within the LCS under mechanical stimulus. Appropriate exercise methods are expected to prevent disuse bone loss caused by space weightlessness and other conditions.