Previous research indicated that fine particulate matter (PM 2.5 ) exposure affected both offspring neurodevelopment and the colonization of gut microbiota (GM), while the underlying mechanism remained unclear. Our study aimed to evaluate the impacts of prenatal PM 2.5 exposure on child cognitive development and investigate the role of neonatal GM colonization in the association. Based on the Shanghai Maternal−Child Pairs Cohort, 361 maternal−child pairs were recruited. Prenatal PM 2.5 exposure concentrations were estimated using a high-spatial-resolution prediction model, and child neurodevelopment was assessed by the Ages and Stages Questionnaire. Multivariable linear regression models, logistic regression models, linear discriminant analysis effect size, and random forest model were applied to explore the associations among PM 2.5 exposure, GM colonization, and children's neurodevelopment. The present study revealed a negative correlation between PM 2.5 exposure throughout pregnancy and child neurodevelopment. Prenatal PM 2.5 exposure was associated with an increased risk of suspected developmental delay (SDD) (OR = 1.683, 95% CI: 1.138, 2.489) in infants aged 2 months. Additionally, potential operational taxonomic unit markers were identified for PM 2.5 -related neurotoxicity, demonstrating promising classification potential for early SDD screening (AUC = 71.27%). Prenatal PM 2.5 exposure might disrupt the composition, richness, and evenness of meconium GM, thereby influencing cognitive development and the occurrence of SDD in offspring. Seven PM 2.5 -related genera, Ruminococcus gnavus group, Romboutsia, Burkholderiaceae Caballeronia Paraburkholderia, Blautia, Alistipes, Parabacteroides, and Bacteroides, were validated as correlated with prenatal PM 2.5 exposure and the occurrence of SDD. Moreover, alterations of GM related to PM 2.5 exposure and SDD might be accompanied by changes in functional pathways of amino acid, lipid, and vitamin metabolism as indicated by differentially enriched species in the Kyoto Encyclopedia of Genes and Genomes.