The alterations of osteon morphology were caused by many factors, such as age, osteoporosis, and physical activity level. It is known that fluid flow in osteon play an important role in osteocyte mechanotransduction and hard tissue health, but less is known about these alterations of osteon morphology affect the response of fluid flow. This study aims at using poroelastic finite element analysis to investigate whether these variations of osteon morphology caused by ageing, osteoporosis, or physical activity level can affect the responses of osteon poroelastic behaviors. In this paper, the COMSOL Multiphysics software was used to establish osteon model with different morphological parameters (shape, cross-section curvature, cross-section area and wall thickness), and the effects of these parameters on the fluid pressure (P) and velocity (V) were investigated. The results showed that the osteon shape had large effects on P and V, and the peak value of P and V increased with the increase of the osteon oblateness. Then, we noticed that, the P and V had obviously positive correlation with cross-section curvature in the same region or lamellar structure in an osteon. The larger cross-sectional area caused a smaller P and V. However, the effects of osteon wall thickness showed the opposite way, the P and V amplitudes increased with the increase of the wall thickness. Significantly, our findings indicated that the wall thickness have a larger effect on P and V than that of the cross-section area. The findings of this work indicate that the alterations of osteon morphology associated with age, osteoporosis or physical activity level had significant influence on P and V in the osteon, and affect the signal transduction in the bone which have the potential research and applications value in treatment osteoporosis and other skeletal diseases.