Gut microbiota (GM), the "second genome," exerts influence on human health by impacting brain function through the gut-brain axis. This interaction involves various mechanisms, including immune regulation, metabolites, and neuronal pathways. The application of the next-generation sequencing technology provides a revolutionary tool for the study of GM, which contributes to a deeper comprehension of the GM-host relationship. Children with cerebral palsy (CP), a common neurological disorder in children, are more likely to develop epilepsy, which can exacerbate CP symptoms, particularly those related to cognitive impairment and gastrointestinal tract, such as constipation. The current study identified specific changes in the GM of children with CP accompanied by epilepsy. Furthermore, both diet and oral microbiota have the potential to influence the composition of the GM. Interventions with probiotics and dietary fiber based on GM can improve constipation and cognition, and this approach may be a potential therapeutic strategy.