Abstract Firmness is an important postharvest quality property of fruit. To investigate the reasons for firmness differences between soft and crisp fruit cultivars, two peach ( Prunus persica L. Batsch) cultivars (soft and crisp) were selected to compare the nanostructures of pectins. Water-soluble pectin (WSP), chelate-soluble pectin (CSP) and sodium carbonate-soluble pectin (SSP) were extracted and nanostructures were conducted and analyzed using atomic force microscopy (AFM). The results show that SSP chain lengths were different between the two cultivars with average SSP lengths of 249 nm and 57 nm for fruit of the crisp and soft cultivars, respectively, while the WSP and CSP chain lengths were not much different. There were no statistical differences for chain heights and widths in the three kinds of pectins between fruit of the two cultivars. All the chain heights were about 1–5 nm. The results indicate that neutral sugar-rich pectins from the primary cell wall of peach flesh might be the cause of the main differences in pectin nanostructures between the two cultivars. The neutral sugar-rich pectins in primary cell walls of peach might also be the reason for firmness differences.