Obesity-induced inflammation can lead to an imbalance in bone formation and resorption. Our previous studies have demonstrated that apple polyphenols (APs) can reduce body weight and inflammation. But their effect on bone is still unclear. In this study, we investigated the protective effects of APs on bone loss in mice with high-fat-diet (HFD)-induced obesity. Forty male C57BL/6J mice were divided into control group (10% fat diet), HFD group (60% fat diet), resveratrol group (60% fat diet), and AP group (60% fat diet). Micro-computed tomography revealed a significant increase in bone volume fraction and bone mineral density, and more trabecular bone and less trabecular bone separation in the AP group compared with the HFD group. In addition, serum tumor necrosis factor (TNF)-α, interleukin-6 (IL-6), and tartrate-resistant acid phosphatase (TRACP) levels were decreased; runt-related transcription factor 2 (Runx2) levels were increased; the collagen area was enlarged; and femur biomechanical property was enhanced in the AP group compared with the HFD group. APs significantly increased the ratio of osteoprotegerin to the receptor activator for the nuclear factor-κB ligand (OPG/RANKL) compared with the HFD group. Resveratrol could also improve the glucolipid regulation, but poorer osteogenic promotion was found compared to APs. The present study demonstrated that APs prevent loss of bone mass induced by obesity, which has potential implications for the prevention and treatment of obesity-related osteoporosis.