The very large G protein-coupled receptor 1 (VLGR1) is a core component in inner ear hair cell development. Mutations in the vlgr1 gene cause Usher syndrome, the symptoms of which include congenital hearing loss and progressive retinitis pigmentosa. However, the mechanism of VLGR1-regulated intracellular signaling and its role in Usher syndrome remain elusive. Here, we show that VLGR1 is processed into two fragments after auto-cleavage at the G-protein-coupled receptor proteolytic site (GPS site). The cleaved VLGR1-β subunit constitutively inhibited adenylate cyclase (AC) activity through Gαi coupling. Co-expression of the Gαiq chimera with the VLGR1-β-subunit changes its activity to the PLC/NFAT signaling pathway, which demonstrates the Gαi protein-coupling specificity of this subunit. A R6002A mutation in intracellular loop 2 (ICL2) of VLGR1 abolished Gαi coupling, but the pathogenic VLGR1 Y6236fsx1 mutant showed increased AC inhibition. Furthermore, overexpression of another Usher syndrome protein, PDZD7, decreased the AC inhibition of the VLGR1-β subunit but showed no effect on the VLGR1 Y6236fsx1 mutant. Taken together, we identified an independent Gαi signaling of the VLGR1-β subunit and its regulatory mechanisms, which may have a role in the development of Usher syndrome.