Background: The aim of this study is to search for the predictive value of 3D fat analysis and calculation technique (FACT) and intravoxel incoherent motion (IVIM) parameters in identifying osteoporosis in women. Methods: We enrolled 48 female subjects who underwent 3.0 T MRI, including 3D FACT and IVIM sequences. Bone mineral density (BMD) values and Fracture Risk Assessment (FRAX) scores were obtained. Proton density fat fraction (PDFF) in the bone marrow and the real diffusion (D) value of intervertebral discs were measured on 3D FACT and IVIM images, respectively. Accuracy and bias were assessed by linear regression analysis and Bland–Altman plots. Intraclass correlation coefficients were used to assess the measurements’ reproducibility. Spearman’s rank correlation was applied to explore the correlation. MRI-based parameters were tested for significant differences among the three groups using ANOVA analyses. A receiver operating characteristic (ROC) analysis was performed. Results: The PDFF of the vertebral body showed a negative correlation with BMD (R = −0.393,p= 0.005) and a positive correlation with the FRAX score (R = 0.706,p< 0.001). The D value of intervertebral discs showed a positive correlation with BMD (R = 0.321,p= 0.024) and a negative correlation with the FRAX score (R = −0.334,p= 0.019). The area under the curve values from the ROC analysis showed that the 3D FACT and IVIM sequences could accurately differentiate between normal and osteoporosis (AUC = 0.88 using the PDFF; AUC = 0.77 using the D value). The PDFF value demonstrated a sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 78.6%, 89.5%, 84.6%, and 85.0%, respectively, in its ability to predict osteoporosis. The D value had a sensitivity, specificity, PPV, and NPV of 63.16%, 92.9%, 65.0%, and 77.8%, respectively, for predicting osteoporosis. Conclusions: The 3D FACT- and IVIM-measured PDFF and D values are promising biomarkers in the assessment of bone quality and fracture risk.