Helicobacter pylori(Hp) is one of the most prevalent gastric pathogens globally, and its eradication effectively reduces the incidence of gastric cancer, peptic ulcers, and related diseases. However, conventional antibiotic therapies, due to their broad-spectrum bactericidal effects, disrupt gut microbiota homeostasis, leading to adverse outcomes such as diarrhea, increased antibiotic resistance, and immune dysfunction. This review systematically explores the bidirectional relationship between Hp eradication therapy and gut microbiota dysbiosis. On one hand, while mainstream bismuth-containing quadruple therapy achieves high eradication rates, it significantly reduces gut microbiota diversity, impairs short-chain fatty acid metabolic pathways, and compromises the protective function of the intestinal barrier. Conversely, Hp infection itself alters the gastric microenvironment through virulence factors, indirectly exacerbating gut microbiota imbalance. Emerging therapies, including vonoprazan-based dual therapy, minocycline-containing regimens, and probiotic adjuvant treatments, mitigate microbiota perturbation but face challenges such as strain-specific efficacy variability and heightened resistance risks. Future strategies should integrate targeted delivery systems, synergistic Chinese-Western medicine approaches, and artificial intelligence to develop personalized regimens that balance eradication efficacy, mucosal repair, and microbiota equilibrium, thereby harmonizing therapeutic outcomes with long-term gut health.