Lung transplantation is a key treatment for end-stage lung diseases, yet postoperative complications often significantly affect long-term survival of recipients. In recent years, the role of the respiratory microbiota in lung transplantation outcomes has gained increasing attention, offering new perspectives for understanding and intervening in post-transplant complications. This article systematically reviews the dynamic changes in the respiratory microbiota of lung transplant recipients from the perioperative period through long-term recovery. Findings indicate that during the perioperative phase, various end-stage lung diseases already exhibit microbiota dysbiosis, characterized by reduced alpha-diversity and enrichment of specific bacterial species. Postoperatively, the microbiota demonstrates temporal and spatial heterogeneity, with changes in its diversity and microbial load correlating with multiple complications. Evidence suggests that microbiota imbalance may exacerbate local inflammation and fibrosis in the lung graft through metabolite-immune interactions, highlighting the potential clinical value of microbiota-targeted interventions. However, establishing long-term dynamic monitoring systems for the microbiota, validating underlying mechanisms, and developing individualized regulatory strategies remain important challenges. Moving forward, integrating multiomics technologies will be essential to advance the field from descriptive observations toward mechanistic insight and clinical translation.