The impacts of microplastics on the gut microbiota, a crucial component of the health of aquatic animals, remain inadequately understood. This phylogenetically controlled meta-analysis aims to identify general patterns of microplastic effects on the alpha diversity (richness and Shannon index), beta diversity, and community structure of gut microbiota in aquatic animals. Data from 63 peer-reviewed articles on the Web of Science were synthesized, encompassing 424 observations across 31 aquatic species. The analysis showed that microplastics significantly altered the community structure of gut microbiota, with between-group distances being 87.75% higher than within-group distances. This effect was significant even at environmentally relevant concentrations (≤1 mg L−1). However, their effects on richness, Shannon index, and beta diversity (community variation) were found to be insignificant. The study also indicated that the effects of microplastics were primarily dependent on their concentration and size, while the phylogeny of tested species explained limited heterogeneity. Furthermore, variations in gut microbiota alpha diversity, beta diversity, and community structure were correlated with changes in antioxidant enzyme activities from the liver and hepatopancreas. This implies that gut microbiota attributes of aquatic animals may provide insights into host antioxidant levels. In summary, this study illuminates the impacts of microplastics on the gut microbiota of aquatic animals and examines the implications of these effects for host health. It emphasizes that microplastics mainly alter the community structure of gut microbiota rather than significantly affecting richness and diversity.