To evaluate the cardiovascular impact of traffic-related pollutant exposure on healthy young adults, the research team has collected the primary data of in-cabin exposure to air pollutants and heart rate variability (HRV). Twenty young healthy college students were recruited in Taipei metropolitan area. In addition to electrocardiogram, personal exposure to air pollutants, i.e., particulate matter (PM) and carbon monoxide (CO), and weather conditions, including temperature and relative humidity (RH), on campus, bus, and mass rapid transit were monitored continuously. The following HRV parameters were evaluated using generalized additive mixed model to adjust for personal and meteorological variables: heart rate (HR), the square root of the mean of the sum of the squares of differences between adjacent normal-to-normal (NN) intervals (r-MSSD), the standard deviation of all NN intervals (SDNN), the percentage of successive NN interval differences greater than 50 ms (pNN50), low-frequency power (LF), high-frequency power (HF), total power (TP), and LF/HF. They were assessed to find out the association between in-cabin exposure and HRV parameters. Compared with the HRV parameters measured on campus, the percent changes in r-MSSD, SDNN, pNN50+1, LF, HF, and TP decreased when the participants were in public transits. After adjusting for all locations, 5 min moving averages of PM2.5–10 and PM1 were significantly associated with the increase in the percent changes in HR and SDNN. Additionally, 5 min moving averages of PM2.5–10 exposure were significantly associated with the decrease in the percent change in HF, while it was significantly associated with the increase of the percent change in LF/HF. The reduction of the percent change in HR was also found to be significantly associated with 5 min CO moving averages. To conclude, current analyses have shown that size-fractionated PMs and CO exposure in public transits might lead to significant changes of HRV parameters for healthy young adults.