Russeting is a commercially important process that restores the control of water loss through the skin via the formation of a waterproofing periderm just beneath the microcracked skin of pear primary fruit. A spontaneous russet skin mutant, the yellow-green ‘Dangshansuli’ pear, has been identified. To understand the role of polyamines in the formation of the russet skin of the mutant-type (MT) pear, it was treated with methylglyoxal-bis-(guanylhydrazone) (MGBG) for 4 weeks after full bloom. One week later, differentially expressed genes among the wild-type (WT), MT, and MGBG-treated MT pears were screened, hydrogen peroxide (H2O2) was localized using CeCl3, and the contents of H2O2 and polyamine were measured. A total of 57,086,772, 61,240,014, and 67,919,420 successful reads were generated from the transcriptomes of WT, MT, and MGBG-treated MT, with average unigene lengths of 701, 720, and 735 bp, respectively. Differentially expressed genes involved in polyamine metabolism and suberin synthesis were screened in ‘Dangshansuli’ and in the mutant libraries, and their relative expression was found to be significantly altered after treatment with MGBG, which was confirmed by real-time PCR. The expression patterns of differentially expressed transcription factors were identified and were found to be similar to those of the polyamine- and suberin-related genes. The results indicated that the H2O2 generated during polyamine metabolism might contribute to russet formation on the exocarp of the mutant pear. Furthermore, the contents of H2O2, spermidine, spermine, and putrescine and H2O2 localization provided a comprehensive transcriptomic view of russet formation in the mutant pear.