To investigate the physiological and molecular properties relating to cell wall carbohydrate metabolism in fruit, the ultrastructure and polysaccharides compositions of the cell wall, as well as the fruit quality and activities of enzymes relating to fruit softening, were studied for three Hami melon varieties ('Xizhoumi 17', 'Jinhuami 25', and 'Chougua') representing three different storability levels. The results showed that 'Chougua' maintained a higher firmness on day 18, with the lowest decay incidence (0%). 'Chougua' showed a better storage quality and intact cell wall structure. The molecular weight and monosaccharide composition of cell wall polysaccharides for Hami melons underwent great changes during storage, and the degradation of pectin polysaccharides was obvious, involving the depolymerization of macromolecular polymers accompanied by the production of new macromolecular polymers and composition changes in pectin monosaccharides (glucose, galactose, and arabinose) during the softening process of the Hami melons. Polygalacturonase, pectin methylesterase, xyloglucan endo-transglycosylase/hydrolase, α-arabinofuranosidase, β-galactosidase, and cellulase were associated with fruit softening at different stages of storage. There were similar softening mechanisms in the three Hami melons. This study will provide reference for further study on the fruit softening mechanisms of Hami melons.