Rapeseed (Brassica napus) is the third-largest oil crop globally, making it crucial to understand the molecular mechanisms behind the thousand-seed weight (TSW) for enhancing its yield and value. Previous studies have identified BnaKINβ1 (β1 subunit of SnRK1 complex) as a candidate gene for TSW. In this study, we employed CRISPR/Cas9-mediated editing of BnaKINβ1 and phenotypic analysis to confirm its role in seed size regulation, and electron microscopy further revealed its function at the cellular level. Integrated transcriptomic and metabolomic analyses revealed that BnaKINβ1 might regulates seed size by influencing sugar metabolism pathways. Protein interaction and ubiquitination assays elucidated the molecular mechanism by which BnaJUL1 (an E3 ubiquitin ligase) mediates the degradation of BnaKINβ1 and BnaKIN10. This study establishes a functional link between BnaKINβ1 and TSW regulation in rapeseed, providing novel insights into the molecular network controlling seed size and offering valuable genetic resources and theoretical foundations for high-yield rapeseed breeding.