Background Currently, the eradication rate of Helicobacter pylori ( H. pylori ) is markedly decreasing due to some antibiotics resistance, including clarithromycin, metronidazole, and levofloxacin. So, there is a considerable interest in evaluating new antibiotic combinations and regimens. Antofloxacin is a novel fluoroquinolone with broad-spectrum antibacterial activity against Gram-negative bacilli including H. pylori . This study is designed to evaluate the efficacy, safety and tolerability of 14-day antofloxacin-based bismuth quadruple therapy as a treatment regimen in Chinese patients with H. pylori infection. Methods We recruited 290 adult patients with H. pylori infection through upper endoscopy and histologic examination. Patients were randomly assigned to receive either antofloxacin-based bismuth quadruple therapy (ACLA therapy, antofloxacin 200 mg once daily, colloidal bismuth pectin 200 mg three times a day, lansoprazole 30 mg twice daily, and amoxicillin 1 g twice daily) for 14 days; or levofloxacin-based bismuth quadruple therapy (LCLA therapy, levofloxacin 500 mg once daily, colloidal bismuth pectin 200 mg three times a day, lansoprazole 30 mg twice daily, and amoxicillin 1 g twice daily) for 14 days. Eradication was assessed by 13 C-urea breath test after six-week treatment, the primary endpoint was the eradication rate by intention-to-treat (ITT) and per-protocol (PP) analyses. Results Allocated to ACLA were 145 (66F/70M, 42.1±12.8 years, 19.3% smokers, 13.1% alcohol drinker) and 145 (64F/81M, 41.1±12.2 years, 17.9% smokers, 12.4% alcohol drinker) patients to LCLA. 13 patients were lost to follow-up and 3 patients took < 80% of treatment drugs. The resistant rates for amoxicillin, levofloxacin and antofloxaci were 4.1% (12/290), 30.3% (44/145) and 0% (0/145), respectively. The ITT analysis showed eradication rates were 93.8% (136/145) in the ACLA group versus 86.2% (125/145) in the LCLA group ( p =0.031). The PP analysis showed eradication rates were 97.8% (136/139) in the ACLA group versus 92.6% (125/135) in the LCLA group ( p =0.000). The ACLA therapy exhibited lower rates of overall adverse events than LCLA therapy (33.8% vs. 42.0%), but the difference was not statistically significant ( p =0. 159). Conclusion Antofloxacin-based bismuth quadruple therapy might be considered as an alternative for the eradication of H. pylori treatment, since it attained a successful eradication rate of 90% which was superior than levofloxacin-based bismuth quadruple therapy. Both regimens were well tolerated and safe.