Background/Objectives: Childhood metabolic dysregulation exerts a profound influence on the development of obesity and metabolic diseases. The human gut microbiota, with highly personalized characteristics, plays an important role in host metabolism. However, the dynamics of gut microbial features during this developmental phase are still unclear. This longitudinal observational study collected 204 fecal samples and 153 blood samples from 51 children (aged 8.90 ± 0.78 years) at four timepoints over 52 weeks, aiming to identify dynamic changes in individual gut microbiota and underlying mechanistic interactions that predict measures of pediatric metabolic health. Methods: Fecal samples were subjected to 16S rRNA gene amplicon sequencing and short-chain fatty acid quantification. Serum samples were analyzed for biochemical tests. Dietary intake, physical activity, clinical phenotypes, early-life factors, and fecal characteristics were further assessed. Results: In the results, the fecal microbiota dynamics exhibit inter-individual variation among children, allowing classification into high- and low-stability subgroups based on intra-individual β-diversity variability. Children with low-stability microbiota had adverse blood lipid profiles (p < 0.05). Compared to the high-stability group, the low-stability microbiota demonstrated significant association with low dietary fiber and highly variable amino acid consumption (|r| > 0.3, q < 0.05). Low-stability microbiota exhibited marked fluctuations in Phocaeicola vulgatus, which was strongly linked to both blood triglycerides and lipoprotein(a) levels, as well as dietary fiber and amino acid intake. Baseline depletion of P. vulgatus and Faecalibacterium duncaniae, combined with the children’s physiological status, lifestyle behaviors, and early-life factors, predicted microbial stability classification (AUROC = 0.93). Conclusions: These findings suggested that the variation in the gut microbiota dynamics could be considered as a possible complementary biomarker to understand the individualized responses within dietary interventions aimed at improving metabolic health in childhood. Further well-designed intervention study is needed to define these observational associations.