Development of effective rescue countermeasures for toxic inhaled industrial chemicals such as methyl isocyanate (MIC) has been an emerging interest. The conducting airways are especially sensitive to such chemicals, and their inhalation can cause severe airway and lung damage. In an attempt to develop an effective therapeutic agent for MIC, animal models have been evaluated with molecular diagnostics, histological examination, and arterial blood gases. However, direct measurement of the airway structure has not been performed. Our group previously demonstrated anatomical OCT scanning of human proximal airways with endoscopic probes. However, a smaller probe with diameter of less than half a millimeter is required for scanning the MIC-exposed rat trachea. In this study, we acquired volumetric scanning of MIC-exposed rat trachea using a miniature endoscopic probe and performed automated segmentation to reconstruct a 3-D structure of the intraluminal surface. Our miniature probe is 0.4 mm in diameter and based on a fully fiberoptic design. In this design, three optical fibers with core sizes of 9, 12, and 20 um replace the lens, and the angle-polished fiber at the distal end reflects the beam at a perpendicular angle and replaces the mirror. Using automated segmentation, we reconstructed the three-dimensional structure of intraluminal space in MIC-exposed rat trachea. Compared to the non-exposed rat trachea, which had a hollow tubular structure with a relatively uniform cross-section area, the MIC-exposed rat trachea showed significant airway narrowing as a result of epithelial detachment and extravascular coagulation within the airway. This technique could potentially be applied to high-throughput drug screening of animal models.