Sensory hearing loss (SNHL) has a high degree of genetic heterogeneity, and there are many mutated genes that cause deafness. GIPC3 gene is one of the mutated genes that can cause congenital hearing loss found in recent years, but the mechanism of its cause is still unclear. Mitophagy is the process of selectively encapsulating and lysing damaged or dysfunctional mitochondria in order to prevent accumulation of damaged mitochondria from damaging the cells and is of great importance in the maintenance of homeostasis in the inner ear. The aim of this paper is to observe the effect of Gipc3 expression on mitochondrial metabolism and autophagy in inner ear hair cells, and to explore the possible mechanism of sensorineural hearing loss caused by Gipc3 mutations. In this study, The House Ear Institute Organ of Corti 1(HEI-OC1) cells and cochlear explants were cultured to change the expression level of Gipc3 by transfection, and the knockdown efficiency was examined by quantitative polymerase chain reaction (qPCR) and Western Blot. Knockdown of Gipc3 inhibited cell viability and its proliferation ability. When t-BHP was used to induce oxidative stress injury and knockdown of Gipc3, inner ear hair cells had weakened ability to resist oxidative stress injury, mitochondrial metabolism was altered, and there was accumulation of reactive oxygen species and reduction of mitochondrial membrane potential. Immunofluorescence and Western Blot techniques revealed that the mitochondrial autophagy-related proteins, LC3B and P62, showed autophagy disorders. A PH domain, leucine zipper motif 1(APPL1) mediates early endosome-dependent mitophagy, and deletion of APPL1 impairs mitochondrial autophagy. We found that fluorescence co-localization exists between Gipc3 and APPL1, and that they interact with each other, with positive correlation in their trends. In summary, Gipc3 mutation may lead to decreased mitochondrial function by inhibiting the APPL1-mediated mitochondrial autophagy process, out of which impaired oxidative metabolism in hair cells may occur, which is a possible mechanism for the inhibition of mitochondrial autophagy by Gipc3 mutation.