Objective To study the effects of intramedullary pressure on the fluid flow behavior in bones. Methods Multi-scale models of macro bone tissue and macro-meso osteon groups were established using The COMSOL Multiphysics software. Considering the interrelationship of different pore scales, such as the bone marrow cavity, Haversia canal, and bone lacunar-canaliculus, the pore pressure and flow rate of hollow bone tissues and bone tissues with intramedullary pressure were compared, and the effects of the amplitude and frequency of intramedullary pressure on the pressure and flow velocity of the liquid in the bone were analyzed. Results When intramedullary pressure was considered, the pore pressure in bone tissues with intramedullary pressure was 6.4 kPa higher than that in hollow bone tissues. The flow pressure increased significantly with an increase in the intramedullary pressure amplitude, but the flow velocity remained unchanged. The frequency of intramedullary pressure had little effect on pore pressure and flow velocity. Conclusions The multi-scale pore model established in this study can accurately analyze bone fluid flow behavior. These results are of great significance for an in-depth understanding of force conduction in the bone.