Obstructive sleep apnea syndrome (OSAS) is prevalent among children and is associated with elevated blood pressure (BP), posing a risk for future hypertension and cardiovascular diseases. While the roles of gut microbiota and systemic inflammation in OSAS pathogenesis are recognized in adults and animal models, their impact on pediatric BP remains less understood. This cross-sectional study explored the relationships between polysomnographic parameters, gut microbiota, systemic inflammation, and BP in 60 children with OSAS. Significant associations between specific microbial profiles—including beta diversity and 31 marker microbes—and BP variations were observed. These microbial profiles correlated with significant alterations in systemic inflammation markers like interleukin-17 and tumor necrosis factor-α. Notably, the relative abundance of Acinetobacter was related to fluctuations in these inflammatory markers and BP levels. The research further highlighted the unique microbial and cytokine profiles exhibited by children with different BP levels, indicating a substantial role of gut microbiota and systemic inflammation in influencing pediatric cardiovascular health. The findings suggest integrating gut microbiota management into comprehensive cardiovascular risk strategies for children with OSAS. This initiative underscores the need for further investigations to decode the mechanisms behind these associations, which could lead to innovative treatments for pediatric OSAS.