Current research indicates that the lungs are not sterile and maintain their own unique microecological balance, which can be disrupted by mechanical ventilation.One-lung ventilation (OLV) induces ischemia-reperfusion (IR) injury in the non-ventilated lung, a common contributor to acute lung injury during the perioperative period. This study investigates alterations in the pulmonary microbiome following one-lung ventilation during thoracoscopic lobectomy and evaluates the impact of differential microbiota on inflammatory responses. Approved by the Hospital Ethics Committee, this study involved 65 patients undergoing thoracoscopic lobectomy from April 2024 to June 2024. An internally controlled paired analysis was implemented to compare bronchoalveolar lavage fluid(BALF) collected from the operative side lung before and after one-lung ventilation. Key outcomes included changes in lung microbiota composition, levels of IL-1 beta and TNF-alpha, and the incidence of postoperative complications, with samples preserved for future analysis. Our research revealed significant changes in the abundances of Veillonella, Rothia, Ralstonia, and Melittanglum following one-lung ventilation during thoracoscopic lobectomy. However, there were no notable changes in overall microbial diversity, and alpha diversity remained unchanged. Correspondingly, the levels of IL-1 beta and TNF-alpha in the bronchoalveolar lavage fluid significantly increased post-OLV, positively correlating with Ralstonia abundance. The operational taxonomic units and species abundances significantly decreased following one-lung ventilation; nevertheless, overall microbial diversity remained stable. In BALF, levels of IL-1 beta and TNF-alpha were markedly elevated, with Ralstonia identified as a key pulmonary microbiome agent influencing inflammatory responses after one-lung ventilation.