Objective To observe the curative effect of Qujun Tongyou Decoction instead of antibiotics in treatment of Helicobacter pylori (HP) associated gastric disease, and explore the mechanism of action. Methods In 236 patients, 140 cases of newly diagnosed patients were randomly divided into treatment group of 80 cases and control group of 60 cases, 96 cases of retreatment patients were randomly divided into treatment group of 56 cases and control group of 40 cases. The control group was given western quadruple therapy:newly diagnosed patients with rabeprazole sodium enteric-coated capsules+colloidal bismuth pectin+Amoxicillin Capsules+clarithromycin dispersible tablets;retreatment patients with rabeprazole sodium enteric-coated capsules+colloidal bismuth pectin+metronidazole tablets+levofloxacin tablets. The treatment group was given rabeprazole sodium enteric coated capsules and colloidal bismuth pectin plus Qujun Tongyou Decoction. All patients were treated for 2 weeks. 1, 3, 6 months after treatment, 14C-urea breath test was detected, HP negative rate, recurrence rate, clinical symptoms, and adverse reaction were observed. Results HP negative rate, the total effective rate and the recurrence rate in treatment group were different with the control group (P<0.05). There was significant difference in the rate of symptom control between treatment group and the control group (P<0.01). No adverse reaction showed in treatment group. Conclusion Rabeprazole sodium enteric-coated capsules and colloidal bismuth pectin combined with Qujun Tongyou Decotion can effectively inhibit and kill HP, promote the repair and healing of ulcer, control symptoms, reduce HP recurrence, lessen adverse reaction, is effective in the treatment of HP associated gastric diseases.