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Inflorescence architecture in rice (<i>Oryza sativa</i>) is mainly determined by spikelets and the branch arrangement. Primary branches initiate from inflorescence meristem in a spiral phyllotaxic manner, and further develop into the panicle branches. The branching patterns contribute largely to rice production. In this study, we characterized a rice <i>verticillate primary branch 1</i>(<i>vpb1</i>) mutant, which exhibited a clustered primary branches phenotype. Gene isolation revealed that <i>VPB1</i> was a allele of <i>RI</i>, that it encoded a BELL-like homeodomain (BLH) protein. <i>VPB1</i> gene preferentially expressed in the inflorescence and branch meristems. The arrangement of primary branch meristems was disturbed in the <i>vpb1</i> mutant. Transcriptome analysis further revealed that <i>VPB1</i> affected the expression of some genes involved in inflorescence meristem identity and hormone signaling pathways. In addition, the differentially expressed gene (DEG) promoter analysis showed that <i>OsBOPs</i> involved in boundary organ initiation were potential target genes of VPB1 protein. Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter system further verified that VPB1 protein bound to the promoter of <i>OsBOP1</i> gene. Overall, our findings demonstrate that <i>VPB1</i> controls inflorescence architecture by regulating the expression of genes involved in meristem maintenance and hormone pathways and by interacting with <i>OsBOP</i> genes.