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This systematic review and meta-analysis aimed to evaluate the effects of a low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet on gut microbiota regulation. A comprehensive literature search was conducted in PubMed, Cochrane Library, Web of Science, Embase, CNKI (China National Knowledge Infrastructure), and Wanfang Data databases. Randomized controlled trials (RCTs) comparing low FODMAP diets with normal diets were included. The primary outcome was the effect on intestinal flora. The standardized mean difference (SMD) with 95% confidence intervals (CI) was calculated using a random-effects model. Heterogeneity was assessed using the I2 statistic, and publication bias was evaluated using funnel plots and Egger's test. Ten RCTs involving 590 participants were included in the analysis. The low FODMAP diet showed a significant positive effect on intestinal flora compared to normal diets (SMD = 0.33, 95% CI [0.01, 0.64], p = 0.003). Substantial heterogeneity was observed (I2 = 67.5%). Subgroup analysis of irritable bowel syndrome (IBS) patients revealed no significant difference between low FODMAP and normal diets (SMD = 0.08, 95% CI [-0.17, 0.32], p = 0.306), with low heterogeneity (I2 = 17.0%). No significant publication bias was detected (Egger's test, p = 0.328). This meta-analysis suggests that a low FODMAP diet may have a positive effect on gut microbiota regulation. However, the effect appears to be less pronounced in IBS patients. Further high-quality studies are needed to confirm these findings and explore the long-term impact of low FODMAP diets on gut health across various gastrointestinal disorders.