Objective To investigate the predictive value of vertebral fat fraction (FF) values from IDEAL-IQ sequences in distinguishing between normal bone mass, osteopenia, and osteoporosis.Methods We recruited 105 women and 69 men over 30 years of age who voluntarily underwent DXA, QCT scans, and MRI examinations and collected clinical information from each subject. Bone mineral density (BMD) values measured by DXA and QCT were used as reference standards. The intra-observer correlation coefficient (ICC) was used to assess the reproducibility of inter-observer and intra-observer measurements. One-way ANOVA, Pearson correlation analysis, and subject work characteristic curve analysis were performed.Results The age, height, weight, BMD, and FF values in the DXA and QCT subgroups were significantly different (P < 0.05). Interestingly, FF was correlated with visceral adiposity (r = 0.221, P = 0.003) in the QCT grouping. FF was moderately negatively correlated with aBMD values (r = − 0.515, P < 0.001; after correcting for gender and age: r = − 0.316, P < 0.001), and FF showed a significant negative correlation with vBMD (r = − 0.790, P < 0.001; after correcting for gender and age: r = − 0.601, P < 0.001). Lumbar FF was positively correlated with age (r = 0.643, P < 0.001). In the DXA subgroup, the area under the curve (AUC) value of the FF values for distinguishing low bone mass was estimated to be 0.714, with a sensitivity of 0.822, a specificity of 0.518, and a cut-off value of 42.85%. In the QCT subgroup, the AUC of the FF values for distinguishing low bone mass was estimated to be 0.869, with a sensitivity of 0.841, a specificity of 0.721, and a cut-off value of 47.97%.Conclusions The vertebral FF value from IDEAL-IQ sequences has the potential to be a new biological marker for the assessment of osteopenia and osteoporosis. The FF value was more effective in assessing low bone mass measured by QCT than DXA, so QCT combined with IDEAL-IQ sequences is superior for obtaining a comprehensive assessment of osteoporosis.