Abstract Du-Zhong, rich in polyphenolic compounds such as lignans, phenolic acid, and flavonoids, is a kidney-tonifying herbal medicine with a long history of safe use for treatment of bone fractures and joint diseases in China. In the present study, we examined whether Du-Zhong cortex extract (DZCE) with graded doses exerted its preventive effects on estrogen deficiency-induced osteoporosis. Eighty 3-month-old female Sprague–Dawley rats were used and randomly assigned into sham-operated group (Sham) and five ovariectomy (OVX) subgroups, i.e. OVX with vehicle (OVX); OVX with 17α-ethinylestradiol (E 2, 25 μg/kg/day); OVX with DZCE of graded doses (100, 300, or 500 mg/kg/day). Daily oral administration of DZCE or E 2 started on week 4 after OVX for 16 weeks. Treatment with DZCE at higher doses (300 or 500 mg/kg/day) was found to be able to significantly prevent OVX-induced decrease in biomechanical quality of femur such as maximum stress and Young's modulus. The mechanical changes were associated with the prevention of a further bone mineral density (BMD) decrease or even with some improvements in microarchitecture. DZCE dose-dependently inhibited total BMD decrease in the femur caused by OVX, which was accompanied by a significant decrease in skeletal remodeling, as was evidenced by the decreased levels of the bone turnover markers osteocalcin (OC), alkaline phosphatese (ALP), deoxypyridinoline (DPD), and urinary Ca and P excretions. μCT analysis of the femoral metaphysis showed that DZCE at the highest doses (500 mg/kg/day) significantly prevents decrease in bone volume/tissue volume (BV/TV), connect density (Conn.D), trabecula number (Tb.N) and trabecula thickness (Tb.Th), and increase in trabecula separation (Tb.Sp) and structure model index (SMI) in OVX rats. We conclude that 16 weeks of DZCE treatment improves bone biomechanical quality through modifications of BMD, and trabecular microarchitecture without hyperplastic effect on uterus, and it might be a potential alternative medicine for treatment of postmenopausal osteoporosis.