Seed germination rate is a key early trait that strongly influences rice yield. Although germination is known to be regulated by classical phytohormones and certain metabolites, the systematic metabolic regulatory network underlying natural variation, especially the key hub metabolites with causal function, still lacks in-depth analysis. In this study, we investigated 56 rice accessions showing pronounced differences in germination performance and systematically identified metabolic pathways associated with germination rate by integrating metabolomic and proteomic analyses. Pathways involved in amino acid metabolism, energy metabolism, and glutathione metabolism were coordinately activated in Rapid Germination (RG) seeds compared with Delayed Germination (DG) seeds. Among them, glutamine was significantly enriched in the RG group. Exogenous application of glutamine selectively and significantly promoted radicle and shoot elongation in a subset of DG varieties, providing direct evidence for a positive causal role of glutamine in seed germination. The variety-specific response further suggests that germination is controlled by a complex, genotype-dependent regulatory network. Together, our results highlight a glutamine-centered metabolic program as an important basis for rapid rice seed germination and provide potential targets for improving early vigor through metabolic engineering and molecular breeding.