Cigarette smoking poses significant health risks, particularly to the airway, which consists predominantly of basal, club, and ciliated cells that are highly susceptible to damage from exogenous stimuli. Traditional in vitro toxicology relies on 2D cell cultures, which lack the structural complexity and functional relevance of airway architecture. As a novel category of tobacco products, the health implications of heated tobacco products (HTPs) remain largely unknown. To address this, 3D airway organoids were developed as a more physiologically relevant in vitro model for evaluating the toxicity of HTPs. Airway organoids derived from mouse lungs were induced to differentiate into various airway cell types and exposed to HTP aerosols. The exposure impaired organoid growth, reduced cell viability, and altered the proportions of secretory, basal, and ciliated cells, effectively replicating the complex cellular damage observed in vivo. Additionally, typical adverse outcomes, such as oxidative stress, inflammation, and genetic toxicity, were induced, paralleling findings from conventional 2D models. These results established the airway organoids as a viable alternative to animal testing for toxicological studies and offer critical insights into the respiratory health risks associated with HTPs.