Femoral neck bone mineral density (FNBMD) is a high risk factor for femoral head fractures, and coffee intake affects bone mineral density, but the effect on FNBMD remains to be explored. First, we conducted an observational study in the National Health and Nutrition Examination Survey and collected data on coffee intake, FNBMD, and sixteen covariates. Weight linear regression was used to explore the association of coffee intake with FNBMD. Then, Mendelian randomisation (MR) was used to explore the causal relationship between coffee intake and FNBMD, the exposure factor was coffee intake, and the outcome factor was FNBMD. The inverse variance weighting (IVW) method was used for the analysis, while heterogeneity tests, sensitivity, and pleiotropy analysis were performed. A total of 5 915 people were included in the cross-sectional study, including 3 178 men and 2 737 women. In the completely adjusted model, no coffee was used as a reference. The ORs for the overall population at ‘< 1’, ‘1–<2’, ‘2–<4’, and ‘4+’ (95% CI) were 0.02 (–0.01, 0.04), 0.00 (–0.01, 0.02), –0.01 (–0.02, 0.00), and 0.00 (–0.01, 0.02), respectively. The male and female population showed no statistically significant differences in both univariate and multivariate linear regressions. In the MR study, the IVW results showed an OR (95% CI) of 1.06 (0.88–1.27), a P-value of 0.55, and an overall F-value of 80.31. The heterogeneity, sensitivity analyses, and pleiotropy had no statistical significance. Our study used cross-sectional studies and MR to demonstrate that there is no correlation or causal relationship between coffee intake and FNBMD.