Russeting occurs via the epidermal suberin accumulation model in the phenol-ester protection system in pears, especially under excessive rainfall. To clarify the role of rain in the russeting mechanism, we applied multi-omics (transcriptome, metabolome, and proteome) integrated analysis from three colored pear cultivars grown under two rainfall conditions, including a no rain control (C) and a rain-abundant (R) treatment. Broad alterations occurred in 29 overlapping differentially expressed genes (DEGs) involved in the response to stress and secondary metabolite biosynthesis. Three overlapping differentially expressed proteins (DEPs) and seven differentially expressed metabolites (DEMs) were identified among the three comparison groups. Cross-comparison of mRNA and protein data revealed co-expression of DEGs and DEPs. Suberin and phenylpropane were markedly enhanced, while cutin biosynthesis and fatty acid elongation were depressed in russet pears under R. In russet pears, the triacontane associated with wax composition was abruptly missing. Moreover, The PpyHHT1 (103966555) gene and encoded protein HHT1 (694406379), which acts as a ‘bridge’ between phenol- and ester- polymerization, had significantly upregulated expression. Collectively, we provide a comprehensive model of the molecular russeting mechanism, which provides powerful insight into russeting and shows the plasticity of plant defenses to cope with the harsh natural environment.