Kawasaki disease (KD) is an acute febrile illness characterized by systemic vasculitis predominantly affecting small- and medium-sized arteries in children, and its etiology and pathogenesis remain unclear. Studies show that gut microbiota dysbiosis can aggravate vascular endothelial injury and systemic inflammation by reducing short-chain fatty acid production and activating the nucleotide-binding domain leucine-rich repeat and pyrin domain-containing receptor 3 inflammasome. Antibiotic use may further disrupt microbial homeostasis, decrease the response rate to intravenous immunoglobulin therapy in KD, and increase the risk of coronary artery lesions. This review systematically summarizes the characteristic alterations of the gut microbiota in KD and the mechanisms by which antibiotics influence disease prognosis via the gut-vascular axis, and provides a theoretical basis for microbiota-targeted interventions.