Purpose: The purpose of this study was to evaluate the diagnostic accuracy when using various base material pairs (BMPs) in dual-energy computed tomography (DECT), and to establish corresponding diagnostic standards for assessing bone status through comparison with quantitative computed tomography (QCT). Methods: This prospective study enrolled a total of 469 patients who underwent both non-enhanced chest CT scans under conventional kVp and abdominal DECT. The bone densities of hydroxyapatite (water), hydroxyapatite (fat), hydroxyapatite (blood), calcium (water), and calcium (fat) (DHAP (water), DHAP (fat), DHAP (blood), DCa (water), and DCa (fat)) in the trabecular bone of vertebral bodies (T11–L1) were measured, along with bone mineral density (BMD) via QCT. Intraclass correlation coefficient (ICC) analysis was used to assess the agreement of the measurements. Spearman’s correlation test was performed to analyze the relationship between the DECT- and QCT-derived BMD. Receiver operator characteristic (ROC) curves were generated to determine the optimal diagnostic thresholds of various BMPs for diagnosing osteopenia and osteoporosis. Results: A total of 1371 vertebral bodies were measured, and QCT identified 393 with osteoporosis and 442 with osteopenia. Strong correlations were observed between DHAP (water), DHAP (fat), DHAP (blood), DCa (water), and DCa (fat)and the QCT-derived BMD. DHAP (water)showed the best predictive capability for osteopenia and osteoporosis. The area under the ROC curve, sensitivity, and specificity for identifying osteopenia were 0.956, 86.88%, and 88.91% with DHAP (water)≤ 107.4 mg/cm3, respectively. The corresponding values for identifying osteoporosis were 0.999, 99.24%, and 99.53% with DHAP (water)≤ 89.62 mg/cm3, respectively. Conclusions: Bone density measurement using various BMPs in DECT enables the quantification of vertebral BMD and the diagnosis of osteoporosis, with DHAP (water)having the highest diagnostic accuracy.