This longitudinal cohort study explored the associations of 25-hydroxyvitamin D [25(OH)D], parathyroid hormone (PTH), and β-C-terminal telopeptide of type 1 collagen (β-CTX) levels with all-cause mortality in centenarians. The study included 952 centenarians (81.4% female). During a median follow-up of 32 months, 752 (78.9%) centenarians died. The estimated 1-year, 3-year, and 5-year survival rates were 80.0%, 45.7%, and 23.6%, respectively. The association of mortality with 25(OH)D was linear, whereas the associations with PTH and β-CTX were J-shaped, with a lower risk below the median levels. Compared with 25(OH)D of ≥30 ng/mL, 25(OH)D < 30 ng/mL was associated with increased mortality (HR 1.52, 95% CI 1.24−1.86, p < 0.001). Compared with PTH of ≤65 pg/mL, PTH > 65 pg/mL was associated with increased mortality (HR 1.30, 95% CI 1.08−1.56, p = 0.005). Compared with β-CTX of <0.55 ng/mL, β-CTX ≥ 0.55 ng/mL was associated with increased mortality (HR 1.30, 95% CI 1.10−1.54, p = 0.002). A higher β-CTX level (even in the clinical reference range of 0.55−1.01 ng/mL) was associated with increased mortality (HR 1.23, 95% CI 1.04−1.47, p = 0.018). Centenarians with 25(OH)D < 30 ng/mL, PTH > 65 pg/mL, and β-CTX ≥ 0.55 ng/mL had a 2.77-fold (95% CI 1.99−3.85, p < 0.001) increased risk of mortality when compared with those with 25(OH)D of >30 ng/mL, PTH < 65 pg/mL, and β-CTX < 0.55 ng/mL. Lower serum 25(OH)D and higher PTH and β-CTX were independently correlated with increased all-cause mortality in Chinese community-dwelling centenarians.