BACKGROUND: Ambient air pollution is a major risk factor for CVDs, and a plausible mechanism is speculated to be alteration of autonomic nervous system (ANS) function. Yet, the short-term effects of air pollution on heart rate variability (HRV), a measure of ANS balance are inconsistent. OBJECTIVE: This study aimed to evaluate the short-term effects of ambient PM2.5 and NO2 on cardiovascular autonomic function, and to determine vulnerable subgroups and temporal trends from repeated HRV and HR measurements over 14 years in the KORA cohort. METHODS: We analyzed data from 4,032 participants in KORA S4 (1999-2001) and 1,912 in KORA FF4 (2013-2014). Air pollution data were from fixed monitoring stations, and HRV indices were derived from 5-minute ECG recordings. Generalized additive models (GAMs) and generalized additive mixed models (GAMMs) were used to assess associations. RESULTS: In S4, each IQR increase in PM2.5 at the 14-day moving average was associated with a 2.32% (95% CI: - 4.41, - 0.19) decrease in SDNN and a 1.20% (95% CI: 0.16, 2.26) increase in HR. By contrast, KORA FF4 showed opposite associations, with a 0.86% (95% CI: 0.02, 1.70) increase in SDNN at lag 4 for PM2.5. Effect modifications by age and smoking status were observed in S4. No statistically significant associations were found in the longitudinal analysis, however, the observed trends were consistent with the effects identified in S4. CONCLUSION: Short-term exposure to PM2.5 and NO2 impacts cardiac autonomic function, with varying effects across study waves due to aging, smoking, medication, and lower pollution levels. Even at low ambient concentrations, these exposures impaired autonomic function via inflammation and oxidative stress, underscoring the importance of stringent air quality standards and lifestyle interventions in reducing cardiovascular risk.