Introduction: Many previous studies have reported a close relationship between body mass index (BMI) and bone mineral density (BMD). However, the effects of fat on bone health remain controversial, particularly for fat tissue distribution.Methods: This study enrolled 18,263 participants who had undergone health examinations. Body composition and BMD were measured using dual-energy X-ray absorptiometry. The relationships of BMI and regional fat percentage with BMD were detected by multiple linear regression and generalized additive models. The risk of low BMD was calculated using logistic regression.Results: There was a negative relationship between the regional fat percentage and FN BMD or LS BMD in both genders (P<0.05). In females, this relationship was bidirectional. Multiple logistic regression analyses showed that the risk for low BMD linearly increased across increasing regional fat percentage quartile categories. In females, the ORs for low LS BMD were 3.095 (95% CI, 2.618-3.658) for hip fat percentage and 1.532 (95% CI, 1.271-1.848) for waist fat percentage. In males, the ORs for low FN BMD were 2.211 (95% CI, 1.831-2.670) for waist fat percentage and 1.998 (95% CI, 1.694-2.355) for hip fat percentage.Conclusions: Overall, the body fat content was a negative predictor of the BMD, and this effect was gender- and location-dependent. In males, waist fat has a greater effect on the FN BMD, whereas in females, hip fat exerts a more negative influence on the LS BMD, which implies a cross-influence between regional fat content and bone mineral density in males and females.