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This study investigated the compositional differences in fecal microbiota between children with and without <i>H. pylori</i> infection and tested whether probiotics-containing yogurt and bacterial eradication improve <i>H. pylori</i>-related dysbiosis. Ten <i>H. pylori</i>-infected children and 10 controls ingested probiotics-containing yogurt for 4 weeks. Ten-day triple therapy plus yogurt was given to the infected children on the 4th week. Fecal samples were collected at enrollment, after yogurt ingestion, and 4 weeks after successful <i>H. pylori</i> eradication for cytokines and microbiota analysis using ELISA and metagenomic sequencing of the V4 region of the <i>16S rRNA</i> gene, respectively. The results showed <i>H. pylori</i>-infected children had significantly higher levels of fecal TGF-β1 than those who were not infected. Eight of 295 significantly altered OTUs in the <i>H. pylori</i>-infected children were identified. Among them, the abundance of <i>F. prausnitzii</i> was significantly lower in the <i>H. pylori</i>-infected children, and then increased after yogurt ingestion and successful bacterial eradication. We further confirmed probiotics promoted <i>F. prausnitzii</i> growth in vitro and in ex vivo using real-time PCR. Moreover, <i>F. prausnitzii</i> supernatant significantly ameliorated lipopolysaccharide-induced IL-8 in HT-29 cells. In conclusions, Probiotics-containing yogurt ingestion and <i>H. pylori</i> eradication can restore the decrease of fecal <i>F. prausnitzii</i> in <i>H. pylori</i>-infected children.