Background <p>While the protective role of body mass index (BMI) in bone mass has been well-documented, the divergent associations between BMI and estimated bone mineral density (eBMD), attributed to its highly heterogeneous nature, remain insufficiently understood.</p> Methods <p>Leveraging the hitherto largest genome-wide summary statistics, we conducted a two-sample Mendelian randomization (MR) to re-evaluate the effect of genetically predicted BMI on eBMD. Then, MR-Clust was applied to examine the potential presence of distinct causal pathways underlying the BMI-eBMD link. Utilizing tissue-partitioned MR, we estimated the distinct effects of separated tissue-specific subcomponents of BMI on eBMD, further supplemented by multivariable MR of body composition phenotypes on eBMD.</p> Results <p>We reconfirmed the significant positive association between genetically predicted BMI and eBMD (<i>β</i>_IVW = 0.13, <i>P</i> value = 1.28 × 10⁻³⁴). Potential distinct causal pathways contributing to the observed total effect were identified by MR-Clust, with some exerting a protective effect while others leading to its deterioration. Tissue-partitioned MR suggested a marginally independent protective association between skeletal muscle-tissue instrumented BMI and eBMD (<i>β</i>_IVW = 0.14, <i>P</i> value = 4.98 × 10⁻²) after accounting for adipose-tissue instrumented BMI, which was supported by the independent association between genetically predicted lean mass and eBMD after accounting for other body composition phenotypes.</p> Conclusions <p>Our results shed preliminary insights into the intricate relationship between obesity and bone mass, highlighting divergent causal pathways underlying the association between BMI and eBMD. Our findings emphasize the potential importance of precision obesity management over merely a general indicator as BMI in future public health strategies for osteoporosis prevention.</p>