Brachypodium distachyon has emerged as a pivotal model system for deciphering the complex agronomic traits of temperate grasses, owing to its compact genome, short life cycle, and high phylogenetic affinity with Triticeae crops. This article systematically reviews the core advances in Brachypodium functional genomics over the past years and their applications in cereal breeding. First, we elucidate the evolution from a single reference genome to a pangenome atlas, alongside innovations in efficient genetic transformation and multiplex CRISPR/Cas9 genome editing toolkits. These breakthroughs have laid a robust foundation for high-throughput gene function analysis. Second, we highlight key mechanistic discoveries in three core areas: (1)dissecting the ferulic acid cross-linking network of the unique grass Type II cell wall to guide biomass energy improvement; (2)revealing the CBF-dependent cold acclimation and ABA-mediated drought signaling pathways to elucidate the environmental adaptation mechanisms of “cool-season” grasses; and (3)serving as a plant pathology model to decipher defense networks against fungal diseases such as wheat rust and Fusarium head blight. Finally, we discuss the potential and pathways for utilizing Brachypodium as a “rapid prototyping platform” to accelerate precision design breeding in crops like wheat and barley, in the context of integrating synthetic biology and artificial intelligence.