Development of effective rescue countermeasures for toxic inhalational industrial chemicals, such as methyl isocyanate (MIC), has been an emerging interest. Nonetheless, current methods for studying toxin-induced airway injuries are limited by cost, labor time, or accuracy, and only provide indirect or localized information. Optical Coherence Tomography (OCT) endoscopic probes have previously been used to visualize the 3-D airway structure. However, gathering such information in small animal models, such as rat airways after toxic gas exposure, remains a challenge due to the required probe size necessary for accessing the small, narrow, and partially obstructed tracheas. In this study, we have designed a 0.4 mm miniature endoscopic probe and investigated the structural changes in rat trachea after MIC inhalation. An automated 3D segmentation algorithm was implemented so that anatomical changes, such as tracheal lumen volume and cross-sectional areas, could be quantified. The tracheal region of rats exposed to MIC by inhalation showed significant airway narrowing, especially within the upper trachea, as a result of epithelial detachment and extravascular coagulation within the airway. This imaging and automated reconstruction technique is capable of rapid and minimally-invasive identification of airway obstruction. This method can be applied to large-scale quantitative analysis of in vivo animal models.