To investigate Lactobacillus acidophilus (L. acidophilus) and Bifidobacterium bifidum (B. bifidum) supplementation to triple therapy for Helicobacter pylori (H. pylori) eradication and dynamic changes in intestinal flora in children with H. pylori infection. One hundred H. pylori-infected children were randomly assigned to two groups: treatment group (n = 43), standard triple anti-H. pylori therapy plus probiotics of L. acidophilus and B. bifidum for 2 weeks followed by taking probiotics for another 4 weeks; control group (n = 45), standard triple anti-H. pylori therapy for 6 weeks. After 6-week treatment, ¹³C-urease breath test was performed and side effects were monitored during the observation period. Quantitative PCR with 16S rRNA-gene-targeted species-specific primers was carried out for the analysis of human intestinal B. bifidum, L. acidophilus, and Escherichia coli (E. coli). As expected, treatment group could significantly enhance the H. pylori eradication rate (83.7 vs. 64.4 %, P < 0.05). B. bifidum, L. acidophilus, and E. coli showed no statistical difference before or after therapy in the treatment group. The number of B. bifidum and L. acidophilus was significantly decreased after 2-week treatment in the control group, but after 6-week treatment it significantly increased and nearly returned to the level before treatment. The number of E. coli increased significantly after 2-week treatment, while after 6-week treatment, it nearly decreased to the level before treatment. L. acidophilus and B. bifidum supplementation is effective for H. pylori eradication compared with triple therapy alone.