Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely diminish fruit quality during cold chain distribution. Seed browning was a major chilling symptom in 36 genotypes of C. annuum fruit screened after storage at 2 °C for 3 weeks. Among them, pepper fruits of chilling-insensitive 'UZB-GJG-1999-51' and -sensitive 'C00562' were treated at 2 °C for 0 or 24 h, respectively. Analyses of integrated transcriptome-metabolome and relative gene expression in seeds obtained from the two genotypes were conducted to identify key factors involved in the seed browning induced by chilling. The relative contents of branched-chain amino acids such as leucine, isoleucine, and valine were significantly increased after chilling. Transcriptome identification showed 3,140 differentially expressed genes (log twofold change > 1.0 and FDR-corrected p value < 0.05) affected by chilling between the two genotypes. Particularly, genes related to jasmonic acid synthesis and signaling were differentially expressed. A regulatory network of jasmonic acid synthesis and signaling, and regulation of ERF family genes might contribute to chilling response in pepper fruit. The results of this study may help facilitate further studies to develop chilling-insensitive peppers and could be a basis for improving postharvest fruit quality.