BackgroundOveraccumulation of chloride (Cl) when plants suffer NaCl causes cell damage and death, and is regulated by Cl–channel protein (CLC). Apple roots are very sensitive to Cl–, but information associated with CLC is limited in apple crop that widely cultivated in the world.ResultsWe identified 9CLCsfrom the apple genome and divided them into two subclasses. Among them,MdCLC-c1promoter contained the largest number ofcis-actingelements associated with NaCl stress, and only the MdCLC-c1, MdCLC-d, and MdCLC-g were predicted that may be Cl–antiporters or channels. Expression analysis ofMdCLCshomologs in the roots ofMalus hupehensisshowed that most of theMhCLCsexpression were response to NaCl stress, especiallyMhCLC-c1expression was upregulated continuously and rapidly expressed during NaCl treatment. Therefore, we isolated MhCLC-c1 and observed it was a plasma membrane-localized protein. TheMhCLC-c1suppression significantly increased sensitivity, reactive oxygen species content, and cell death of apple calli; whileMhCLC-c1overexpression decreased sensitivity, reactive oxygen species content, and cell death of apple calli andArabidopsisby inhibiting intracellular Cl–accumulation under NaCl stress.ConclusionsThe study selected and isolated aCLC-cgeneMhCLC-c1fromMalus hupehensisbased on identification ofCLCsgene family in apple, and their homologsMhCLCsexpression patterns during NaCl treatments, revealing thatMhCLC-c1alleviates NaCl-induced cell death by inhibiting intracellular Cl–accumulation. Our findings confer the comprehensive and in-depth upstanding of the mechanism that plants resist salt stress, and might also confer genetic improvement of salt tolerance in horticultural crops and the development and utilization of saline–alkali land.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04270-3.