This study identified a RING-type E3 ligase SGD1 and its E2 partner SiUBC32, responsible for grain yield control in *Setaria italica*. SGD1 ubiquitinates the brassinosteroid receptor BRI1, stabilizing it and promoting growth. Overexpressing an elite SGD1 haplotype improved grain yield by about 12.8%. The SiUBC32-SGD1-BRI1 module contributes to grain yield improvement and provides a strategy for exploring key genes in Poaceae crops.