Cardiopulmonary bypass (CPB) is an indispensable technique in cardiac surgery; however, its impact on gut microbiota and metabolites remains insufficiently studied. CPB may disrupt the intestinal mucosal barrier, altering the composition and function of gut microbiota, thereby triggering local immune responses and systemic inflammation, which may lead to postoperative complications. This narrative review examines relevant literature from PubMed, Web of Science, Google Scholar, and CNKI databases over the past decade. Keywords such as “gut microbiota,” “cardiopulmonary bypass,” “cardiac surgery,” and “postoperative complications” were employed, with Boolean operators used to refine the search results. The review examines changes in gut microbiota before and after CPB, their role in postoperative complications, and potential strategies for modulation to improve outcomes.