This case-control study aimed to examine the effect of high serum parathyroid hormone (PTH) level, especially the effect of secondary hyperparathyroidism (SHPT) related to hypovitaminosis D, on bone metabolism and bone phenotypes. We included a total of 830 Chinese postmenopausal women aged ≥ 50 years with serum 25-hydroxyvitamin D (25(OH)D) level < 30 ng/ml, among whom 415 women had prevalent vertebral fractures (VFs) and others were age-matched controls. We measured serum levels of 25(OH)D, PTH and bone turnover markers (BTMs), which included C-terminal telopeptide of type I collagen (β-CTX), N-aminoterminal prepeptide of type I procollagen (P1NP) and osteocalcin (OC). Bone mineral densities (BMDs) at lumbar spine and femoral neck were quantified by dual-energy X-ray absorptiometry. Morphometric VFs were validated by lateral radiograph of thoracolumbar spine. Compared to fracture-free controls, women with VFs exhibited a higher serum level of PTH and a higher percentage of SHPT (both p < 0.05), but had a similar serum level of 25(OH)D (p = 0.166). Positive correlations were depicted between PTH and BTMs (all p < 0.01), and between 25(OH)D and bone formation markers (p = 0.013 for OC, p = 0.068 for P1NP), whereas no significant correlation was identified between both calciotropic hormones and BMDs or between 25(OH)D and β-CTX (all p > 0.05). Increasing PTH was associated with an increased risk of VFs independent of 25(OH)D and BMD [odds ratio (OR) per SD increase in PTH 1.016, 95% confidence interval (95% CI) 1.006-1.027]. Moreover, women with SHPT (i.e., > 68 pg/ml) had about three times odds for VF compared to women with normal PTH levels (OR 3.270, 95% CI 1.581-6.760). These data suggest that evaluated serum PTH level might promote the bone remodeling and then lead to increased risks of VFs among Chinese postmenopausal women with vitamin D insufficiency.