In this study, we investigated microvascular perfusion status, changes to fat content and fatty acid composition in the bone marrow of rat femurs after total-body irradiation by quantitative permeability parameters of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and ex vivo high-resolution magic angle spinning (HRMAS) ¹H nuclear magnetic resonance spectroscopy (NMRS). Thirty-six Sprague-Dawley rats were randomly assigned to either an irradiated or nonirradiated control group. Permeability imaging using DCE-MRI and HRMAS ¹H NMRS was performed before irradiation, as well as at days 4 and 7 postirradiation. The volume transfer constant (K^trans) values increased to 2.219 ± 0.418/min (P < 0.01) at day 4 and to 2.760 ± 0.217/min at day 7 (P < 0.01) postirradiation. The plasma fraction (v_p) values gradually decreased. The proportion of (n-6) polyunsaturated fatty acids (PUFA) gradually reached a peak at day 7, the proportion of (n-3) PUFA gradually decreased and the proportion of saturated fatty acids gradually increased. After irradiation, K^trans at different times showed significant negative correlation with (n-3) PUFA (r = –0.6393, P < 0.01) and significant positive correlation with (n-6) PUFA (r = 0.6841, P < 0.05). These findings indicate that bone marrow microcirculation perfusion and vascular permeability correlated with fat content at an early time point after irradiation. A pathophysiological mechanism may exist based on fat-vascular permeability in the case of injury to bone marrow microcirculation.