Early-life gut microbiome assembly is a pivotal determinant of lifelong health; however, the integrated frameworks governing this process across developmental milestones remain insufficiently defined. This review establishes a multidimensional framework by delineating the crosstalk between the gut microbiome and the host throughout the preconception, prenatal, postpartum, and early childhood stages. We first highlight the emerging paradigm of biparental microbial contributions during the preconception period, detailing how paternal and maternal niches jointly prime offspring development. Moving into pregnancy, we examine the maternal reservoir, integrating the role of gut microbiota-derived metabolites across multiple trimesters in prenatal priming and vertical transmission. For the postpartum period, we discuss the development of the multikingdom gut microbiome and address the impacts of delivery modes and clinical interventions. Here, we articulate a critical knowledge gap: the discrepancy between taxonomic "catch-up" and true functional restoration, particularly in vulnerable cohorts such as preterm infants. Furthermore, we propose a "developmental synchronization" model within the maternal-infant-microbiome continuum. This model posits that early-life "windows of opportunity" are defined by the obligate temporal coupling of host physiological maturation with stage-specific microbial metabolic signals. From a translational perspective, we discuss how this framework informs the development of precision interventions, such as stage-specific probiotics, prebiotics, or metabolic modulators. These therapies aim to restore not only the microbial composition but also the synchronized functional dialog between the microbiome and host development. By mapping the "microbiota-metabolite-host target-physiological phenotype" network, we provide a systematic roadmap for precision-targeted interventions during the first 1000 days of life.
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