Alveolar bone loss is generally considered as a chronological age-related disease. As biological ageing process is not absolutely determined by increasing age, whether alveolar bone loss associated with increasing chronological age or biological ageing remains unclear. Accurately distinguishing whether alveolar bone loss is chronological age-related or biological ageing-related is critical for selecting appropriate clinical treatments. This study aimed to identify the relationship between alveolar bone loss and body ageing. 3635 participants from National Health and Nutrition Examination Survey and 71 living kidney transplant recipients from Gene Expression Omnibus Datasets were enrolled. Multivariate regression analysis, smooth curve fittings and generalized additive models were used to explore the association among alveolar bone loss, age, serum α-Klotho level, renal function markers, as well as between preoperative creatinine and renal cortex related α-Klotho gene expression level. Meanwhile, a two-sample Mendelian randomization study was conducted to assess the causal relationship between α-Klotho and periodontal disease (4,376 individuals versus 361,194 individuals). As biological ageing related indicator, α-Klotho level was negatively correlated with impaired renal function and alveolar bone loss. Correspondingly, accompanied by decreasing renal function, it was manifested with down-regulated expression level of α-Klotho in renal cortex and aggravated alveolar bone loss. The MR analysis further identified the negative association between higher genetically predicted α-Klotho concentrations with alveolar bone loss susceptibility using the IVW (OR=0.999, P=0.005). However, an inversely U-shaped association was observed between chronological age and alveolar bone loss, which especially stable in men (the optimal cut-off values were both 62 years old). For male above 62 years old, increasing age converted to protective factor and accompanied by alleviated alveolar bone loss. Alveolar bone loss which directly associated to decreased renal function and α-Klotho level was related to biological ageing rather than chronological age. The renal-alveolar bone axis could provide new sight of clinical therapy in alveolar bone loss.