Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high heterogeneity and has a prevalence of 0.7% to 3.2% in children. Gut microbiota are a collection of microorganisms that inhabit in human guts, which can produce various metabolites that affect the homeostasis and functions of nervous and endocrine systems. There are many studies on the relationship between various gut microbiota and ASD, but the alteration pattern of microbial profiles in ASD children is not conclusive. In order to more robustly describe the deregulations of gut microbiota compositions in ASD, a meta-analysis was performed. The related investigations from PubMed, Embase and Web of Science were collected and manually reviewed. By procedure, 26 eligible studies until 2023, with a total of 1021 ASD and 951 typically developed children and adolescents, were included for the meta-analysis. RevMan5.4 was used to assess the overall effect of 8 microbes at the phylum level and 19 microbes at the genus level. Results demonstrated relatively up-regulated abundance of Bacteroidetes, Verrucomicrobia, Bacteroides, Clostridium, Dorea and Sutterella, and down-regulated abundance of Proteobacteria, Bifidobacterium, Coprococcus, and Akkermansia in ASD children, indicating partly agreement in the ASD-associated microbes, albeit the heterogeneity of ASD.