The inhibiting effect of chitosan coating (2%) on the softening and sodium carbonate-soluble pectin (SSP) evolution of sweet cherries during non-isothermal storage was investigated. Chitosan coating significantly extend the softening (6.4% greater than the control group), maintained the SSP content (6.6% greater than the control group), and reduced the degradation of SSP by inhibiting the expression of the paPME1–5 genes, which regulating pectin methylesterase activity of sweet cherries under temperature variation. In addition, the results of methylation and monosaccharide composition indicated that the chitosan coating reduced demethylation of SSP and the loss of RG-I main and side chain neutral sugars. Atomic force microscopy images revealed that the coated sweet cherries contained more linked, branched, and long SSP chains and maintained the width of the pectin backbone (>140 nm). These results indicated that a chitosan coating is feasible to preserve postharvest fruit under non-isothermal conditions.;Highlights•Temperature variation accelerated sweet cherry softening and pectin degradation.•Chitosan coating extended sweet cherry firmness loss in non-isothermal conditions.•Chitosan coating reduced the expression of pectin methylesterase-related genes.•Chitosan coating alleviated nanostructure degradation of pectin in sweet cherry.