Both spinal cord injury and ovariectomy can result in ostepenia in rats. SCI induces more deterioration of cortical geometric structure and trabecular microstructure in the proximal tibial metaphysis than OVX. The proximal tibial metaphysis microstructure significantly correlates with its biomechanical properties. Introduction The purpose of the present study was to compare the effects of spinal cord injury (SCI) and ovariectomy (OVX) on bone gain in young female rats. Methods Thirty young female Sprague-Dawley rats were randomized into three groups: age-matched intact control (CON), OVX and SCI. The tibiae were assessed for DXA and micro-CT analysis, biomechanical testing, the upper tibial epiphyseal plate height, and blood samples for biochemical analysis. Results SCI rats showed lower aBMD in the proximal tibiae as compared with OVX rats. Cortical geometric structural parameters of the tibial midshaft in SCI rats were significantly lower than OVX rats. SCI or OVX induced significant changes in all trabecular microstructural parameters in the proximal tibial metaphysis. The trabecular separation (Tb.Sp) and structure mode index (SMI) in SCI rats were significantly higher than in OVX rats. BV/TV explained 84% of the variation of ultimate load of the proximal tibial metaphysis. There was no difference of the upper tibial epiphyseal plate height between SCI and OVX rats. Serum NTX level in SCI rats was significantly higher than in OVX rats. Conclusions SCI induces more deterioration of cortical bone geometric structure and trabecular microstructure in the proximal tibial metaphysis than OVX.