The transportation environment is one we are exposed to every day. However, previous research on exposure to volatile organic compounds (VOCs) and their acute health effects in various public transportation is limited. To address this gap, we conducted a panel study involving 25 healthy adults, investigating the exposures and acute health effects of exposures to 24 VOC species during 40-min commutes in Beijing’s subways, buses and taxis during early spring 2023. Our findings revealed that exposure to multiple VOC species, including toluene, styrene, tetrachloroethylene, ethylacetate, resulted in a decrease in Heart Rate Variability (HRV). Specifically, SDNN decreased by 4.37 ms (95%CI: -8.52, -0.21) with per interquartile range (IQR) increase in ethylacetate; rMSSD decreased by 9.93 ms (95%CI: -19.01, -0.86), 4.75 ms (95%CI: -8.63, -0.86), and 7.00 ms (95%CI: -13.20, -0.81) with per IQR increase in toluene, styrene, and tetrachloroethylene, respectively; HF decreased by 154.07 ms2 (95%CI: -284.03, -24.11) with per IQR increase in carbon tetrachloride. For joint effect of these VOC species, we found significant associations with HRV only in taxis. Moreover, higher cyclohexane and methylcyclohexane exposures were linked to reports of sick car syndrome. Despite wearing masks during the COVID-19 period, comparative results from a supplementary experiment conducted post-COVID-19 without masks indicated that masks may not significantly reduce the adverse effects of VOC exposure. Our findings indicated the potential acute health risks of short-term VOC exposures in public transportation, particularly in taxis, highlighting the necessity to improve air quality and related standards in these micro-environments.