Resistant starch (RS) has attracted much researchers’ attention because of its health-beneficial effects. Gut microbiota obviously shapes human health, but the effects of RS supplementation on the changes of human gut microbiota remain unclear. This observational meta-analysis aimed to reveal the effects of RS intake on α-diversity and composition of gut microbiota through meta-analysis. Two independent authors systematically searched articles from inception until February 2023 on four electronic databases. Twenty-four highly relevant trials were included conforming to Preferred Reporting Items for Systematic reviews and Meta-Analysis protocol, and a total of 816 individuals were included. Significant heterogeneity analyses revealed that RS intake notably decreased Shannon index (weighted mean difference (WMD): –0.11; 95% confidence interval (CI): –0.21, –0.01), and stimulated the composition of health promoting bacteria genera, including Bifidobacterium (relative abundance: WMD: 1.75; 95% CI: 0.39, 3.11; bacterial populations: WMD: 0.36; 95% CI: 0.04, 0.69), Faecalibacterium (relative abundance: WMD: 0.70; 95% CI: 0.20, 1.20; fold change: effect size: 0.91; 95% CI: 0.60, 1.23), and Prevotella (relative abundance: WMD: 0.35; 95% CI: 0.01, 0.69). Taken together, the present study revealed that changes in the gut microbiota diversity and genera were correlated with RS supplementation, which may contribute to benefits in human health.