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Inflammatory bowel disease (IBD)-associated pulmonary injury is one of the frequently underestimated extraintestinal manifestations in clinical practice. It can present as subclinical pulmonary function abnormalities, radiographic changes, or overt inflammatory pulmonary diseases and often overlaps with infection- and treatment-related pulmonary toxicity, complicating early recognition and differential diagnosis. Growing evidence indicates that IBD-associated pulmonary injury is not an isolated pulmonary event but rather a cross-organ pathological process jointly driven by disruption of the intestinal mucosal barrier, dysbiosis, and aberrant microbial metabolites, systemic inflammation, and abnormal immune cell trafficking. This article provides a comprehensive review of current basic and clinical research evidence regarding intestinal barrier dysfunction, bidirectional gut-lung axis regulation, immune remodeling mediated by microbial metabolites, such as short-chain fatty acids (SCFAs), and the mechanisms and differential diagnosis of drug-induced pulmonary injury in IBD treatment. Existing studies suggest that SCFAs, tryptophan metabolites, immune cell homing, and alterations in the local pulmonary microbiota may represent key regulatory nodes in IBD-associated pulmonary injury; however, prospective studies integrating intestinal inflammatory activity, circulating biomarkers, pulmonary phenotypes, and drug exposure are still lacking. In the future, emphasis should be placed on establishing a stratified diagnostic framework for distinguishing pulmonary involvement intrinsic to the disease, infection, and drug-induced pulmonary injury, and on evaluating precision intervention strategies targeting microbial function, metabolite supplementation, and barrier repair to advance the translational application of mechanistic research on IBD-associated pulmonary injury into clinical practice.