Accumulation of body fat is known to be beneficial to bone mass through increased body weight. However, not all the skeleton is loaded by body weight. Therefore, we assume that fat stores would exert different effects on bone mass at different skeletal sites. In this study, 84 perimenopausal Chinese women were recruited. Using dual-energy X-ray absorptiometry, total body fat mass (TBFM), total body lean mass (TBLM), percent body fat (PBF), and total body and regional bone mineral density (BMD) were measured. Correlation analysis indicated that PBF correlated negatively with BMD at ribs and both arms (all P < 0.05). After adjusting for TBLM, PBF had a significantly negative correlation with BMD at head, ribs, both arms, and whole body (all P < 0.05). With adjustment for body weight and height, a significantly negative correlation between PBF and BMD was present, not only at ribs and arms but also at legs and whole body (all P < 0.05, except right leg, at P = 0.094). There was a significantly positive correlation between body weight and leg BMD (all P < 0.001). Body weight was positively correlated with TBFM (r (2) = 0.783, P < 0.001) and TBLM (r (2) = 0.770, P < 0.001). Based on the results, we conclude that increased body fat stores would exert a detrimental effect on BMD, but this effect is more prominent on non-weight-bearing bone. On weight-bearing bone, the detrimental effect of increased body fat could be offset or outweighed by the beneficial effect of increased body weight.