Aims <p>Silicon fertilizer (SF) has been evidenced to promote crop healthy growth and increase yield. However, the interaction effects of SF combined with chemical fertilizer&#xa0;(SF-CF) on rice seedling&#xa0;growth and soil microbial metabolic characteristics remain unclear. This study aims to investigate the interactive effects of SF-CF on rice biomass, soil properties, and the synergistic action of rhizosphere soil microorganisms on the silicon (Si) bioavailability to rice.</p> Methods <p>Five concentrations of SF-CF were used in this experiment. Soil properties, rice seedling&#xa0;growth and microbial carbon use efficiency (CUE) were subsequently analyzed.</p> Results <p>SF-CF significantly promoted rice seedling growth. Compared with CK, the treatment with 300 kg Si ha⁻¹ and 750 kg NPK ha⁻¹ remarkably increased plant height (36%), fresh weight (81%), chlorophyll content (SPAD) (81%) and root development. Although the combined fertilization led to soil acidification, it substantially raised soil organic matter (SOM) (50%-68%) and available Si (18%-42%). Moreover, D-Mannitol and L-Phenylalanine as the most important carbon source for microorganisms and exhibited high stability under different SF-CF inputs.</p> Conclusions <p>SF-CF effectively promoted rice seedling growth and nutrient uptake, while also improving microbial CUE. These findings extend the role of SF from traditional plant nutrition enhancement to soil microbial function regulation and support sustainable agricultural practices.</p> Graphical Abstract <p></p>