Vehicular emissions are a primary source of volatile organic compounds (VOCs), which drive urban ozone and secondary organic aerosol formation while posing direct risks to human health. Progressive emission standards and the widespread adoption of hybrid electric vehicles have successfully reduced total hydrocarbon outputs, establishing them as central strategies for climate and air quality management. However, the influence of these technological shifts on the molecular speciation of emissions—and their associated environmental and toxicological trade-offs—remains poorly understood, potentially masking hidden health risks. Here we apply a concentration-reactivity-toxicity framework to characterize species-resolved VOC emissions across conventional and hybrid vehicles under progressive emission standards. While stricter regulations reduced total VOC emissions by 75% in conventional vehicles, the relative contribution of highly reactive oxygenated VOCs (OVOCs) surged from 20% to 35%. Notably, a modern hybrid vehicle emitted nearly twice the mass of OVOCs (25.4 mg km⁻¹) compared to its conventional counterpart (13.3 mg km⁻¹), driven by frequent engine start–stop cycles that reduce aftertreatment efficiency. This distinct operational profile allows us to identify specific compounds—namely, vinyl acetate and methyl t-butyl ether—as molecular markers for hybrid powertrains in our study. Consequently, despite superior fuel economy, this tested hybrid vehicle exhibited a 69% increase in non-carcinogenic health risks and nearly double the carcinogenic risk, overwhelmingly dominated by aromatics and toxic OVOCs such as acrolein. Furthermore, while absolute emissions declined, persistent aromatics continued to account for over 70% of the secondary organic aerosol formation potential. These findings highlight a critical tension between fuel efficiency advancements and toxicological impacts, suggesting that future emission regulations must transition from total mass limits to species-specific controls to fully safeguard public health.