<p>Advanced biological aging is linked to a higher risk of adverse health outcomes; however, its association with kidney stone (KS) remains unclear. This cross-sectional study investigated the relationship between biological aging acceleration (BAA) and KS, along with the potential mediating role of insulin resistance, in 18,868 Chinese adults aged 20–80 years undergoing health examinations at Ruijin Hospital between 2020 and 2024. Biological age was assessed using the Klemera-Doubal method biological age (KDM-BA) and Phenotypic age(PhenoAge) algorithms, with BAA calculated via residual analysis relative to the chronological age. Insulin resistance(IR) was evaluated using surrogate indices including the triglyceride glucose index (TyG), TyG-body mass index (TyG-BMI), and metabolic score for insulin resistance (METS-IR). The overall prevalence of KS was 5.25%. After full covariate adjustment, participants in the highest quintile of KDM-BA acceleration had a 1.34-fold higher risk of KS than those in the lowest quintile (95% confidence interval [CI]: 1.05–1.70). Similarly, those in the highest PhenoAge acceleration quintile exhibited a 1.39-fold increase in KS risk (95% CI: 1.10–1.76). KDM-BA and PhenoAge acceleration increased by 12% (odds ratio[OR]: 1.12, 95% CI: 1.04–1.20) and 9% (OR: 1.09, 95% CI: 1.03–1.16) per standard deviation, respectively, in correlation with higher KS risk. Restricted cubic spline analysis confirmed dose-response relationships for both KDM-BA (<i>P</i>-_overall=0.002) and PhenoAge acceleration (<i>P</i>-_overall=0.007) with KS. Mediation analysis indicated that IR accounted for 7–13% of these associations. These results imply that an increased risk of KS is linked to accelerated biological ageing, with IR playing a role in this association in Chinese adults. Metabolic and aging monitoring should be enhanced in patients with KS.</p>