The fruit of the ‘Dangshansuli’ pear has a greenish yellow skin, whereas its mutant, the ‘Xiusu’ pear, has a russet skin, which represents a genetic variation. It has been demonstrated that the formation of russet fruit in the ‘Xiusu’ pear is related to lignin accumulation in skin exocarp cells. In this study, we localized hydrogen peroxide (H2O2) to the cell wall using transmission electron microscopy (TEM) and quantified the concentrations of H2O2 and polyamines. In addition, the expression levels of genes involved in polyamine biosynthesis were measured in the exocarps of samples of young fruits of ‘Dangshansuli’, ‘Xiusu’, ‘Xiusu’ treated with methylglyoxal bis(guanylhydrazone), and ‘Xiusu’ treated with ethephon. The results obtained could explain the mechanism by which H2O2 participates in polyamine metabolism in the lignification of exocarp cells in the russet fruit mutant. The TEM results showed that free H2O2 is present near the cell wall, where lignin is primarily synthesized, and the H2O2 concentration was highly positively correlated with the lignin concentration. Although H2O2 related to lignification showed no significant correlation with the putrescine or spermine concentration, it was highly positively correlated with the spermidine (Spd) concentration. Additionally, the Spd concentration was significantly positively correlated with altered expression of the polyamine oxidase gene (PbPAO). Taken together, these results have demonstrated that H2O2 involved in lignification originates from the oxidation of Spd by the enzyme PAO, with high expression of the PbPAO gene, which suggests that H2O2 from polyamine metabolism affects lignification in the exocarp of the russet mutant pear.