Background <p>Cognitive impairment is a major public health problem. This study aimed to examine the association between long-term visit-to-visit resting heart rate variability (RHRV) and cognitive dysfunction among the general population.</p> Methods <p>Data was derived from the Health and Retirement Study (HRS) and the China Health and Retirement Longitudinal Study (CHARLS). Variation independent of mean (VIM) was used to assess participants’ RHRV in the main analyses. Cognitive functions in both cohorts were measured by using tests including memory, attention, and orientation, and a standardized Z score was calculated. Linear mixed models and restricted cubic splines were adopted to explore the association between RHRV and cognitive decline.</p> Results <p>There were 7,582 and 4,085 eligible participants from the HRS and the CHARLS in the analyses, respectively. After adjusting for covariates, VIM of RHRV was significantly associated with global cognitive function (HRS: β for per-SD increment = − 0.022 [95% CI, − 0.040 to − 0.005]; CHARLS: β for per-SD increment = -0.023 [95% CI, − 0.045 to − 0.000]). Similar results were observed from several sensitivity analyses, including using average real variability and coefficient of variation for RHRV, additionally adjusted for physical activity, excluding participants who had heart problems at baseline, and further adjusting for the C-reactive protein in the CHARLS.</p> Conclusion <p>Our results suggest that RHRV was independently associated with cognitive function in the general population.</p>