The gut microbiota has been found to interact with the brain through the microbiota-gut-brain axis, regulating various physiological processes. In recent years, the impacts of the gut microbiota on neurodevelopment through this axis have been increasingly appreciated. The gut microbiota is commonly considered to regulate neurodevelopment through three pathways, the immune pathway, the neuronal pathway, and the endocrine/systemic pathway, with overlaps and crosstalks in between. Accumulating studies have identified the role of the microbiota-gut-brain axis in neurodevelopmental disorders including autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), and Rett Syndrome. The major aims of this review are to, first of all, discuss the mechanisms of the microbial regulation of neurodevelopment alongside the aforementioned three pathways on both the molecular and systemic scales; and second of all, present evidence for the roles of the microbiota-gut-brain axis in various neurodevelopmental disorders, the underlying mechanisms, and the potential therapeutic methods. Finally, we discuss the current situation in the field and propose the paucity in the exploration of the specific mechanisms of the microbiota-gut-brain axis in neurodevelopmental disorders.