Early childhood, spanning from the prenatal period to three years of age, represents a critical window for the coordinated development of the gut microbiota and the immune system. These two systems form a bidirectional regulatory network via the gut-immune axis, which plays a significant role in lifelong health. The gut microbiota matures progressively through four stages: prenatal preparation, initial colonization, stable diversification, and dynamic equilibrium. Concurrently, the immune system establishes immune tolerance and refines its functional capabilities. The microbiota regulates immune cell differentiation through metabolites and molecular interactions, while the immune system reciprocally shapes the structure of the microbiota. Exogenous factors such as mode of delivery, feeding practices, and antibiotic use can influence this synergistic process. Disruption of this balance may increase the risk of allergic, digestive, and metabolic disorders. Targeted strategies, including probiotic supplementation and dietary interventions, can provide a scientific foundation for promoting early childhood health. Research on the underlying mechanisms and interventions also lays the groundwork for clinical translation.