Background <p>Parent-child separation is a risk factor for children’s physical and mental problems, limited literature has explored the impact on children’s development across generations. Here, we examine the effects of intergenerational parent-child separation on accelerating biological aging in preschool children, as indicated by the accelerated eruption of the first permanent molar (M1) and oral epithelial cell telomere length (TL).</p> Methods <p>This study draws on data from a child growth cohort established in rural areas of Anhui Province, China, which included 2,367 children aged 3–6 years. Researchers collected data on parent-child separation experiences and demographic characteristics of both parents and offspring, followed by comprehensive physical and oral examination. Parent-child separation during the parents’ childhood and their children’s separation experiences were recognized as distinct generational exposures, while intergenerational continuity of parent-child separation was defined as both generations experiencing separation. During dental examinations, M1 eruption was classified as accelerated if occurring before 6.1 years in girls or 6.3 years in boys. A follow-up oral examination was conducted six months later, with oral epithelial samples collected for TL measurement.</p> Results <p>Children with missing data, deciduous dentition or undetermined M1 eruption status were excluded, yielding a final sample of 895 children (mean [SD] age: 6.01 [0.14] years). Among these, 179 (20%) experienced intergenerational continuity of parent-child separation. The included children with a mean (SD) age of 6.01 (0.14) years. The overall prevalence of accelerated M1 eruption was 28.7% (257/895). Children exposed to intergenerational continuity of parent-child separation showed a 2.03-times increased risk of accelerated M1 eruption (95% CI: 1.24–3.33, <i>p</i> = 0.005), and 23% shorter telomeres (95% CI: -0.32 to -0.14, <i>p</i> &lt; 0.001) compared to unexposed children. Sensitivity analyses revealed that both paternal and maternal transmission contributed to accelerated biological aging in the oral cavity, though paternal transmission showed stronger effects.</p> Conclusion <p>Our findings demonstrate that intergenerational parent-child separation adversely impacts biological aging in the oral cavity of preschool children. These results underscore the critical need to break the intergenerational cycle of parent-child separation in children’s oral health and overall health.</p> Graphical abstract <p></p>