'Xuxiang' kiwifruit is highly susceptible to chilling injury (CI) during prolonged low-temperature storage, significantly impacting its storage quality and shelf life. Methyl jasmonate (MeJA) has emerged as a pivotal signaling molecule for alleviating CI in fruit. In this study, we conducted a comparative analysis of the changes in physiological and biochemical indicators and related differentially expressed genes (DEGs) through transcriptomics in kiwifruit treated with 10 μM MeJA during low-temperature storage. The results demonstrated that exogenous MeJA effectively alleviated the symptoms of CI in kiwifruit by suppressing the activity of membrane lipid peroxidation-related substances and enzymes, as well as regulating multiple genes associated with ethylene biosynthesis, cell wall degradation, plant hormone signal transduction, and relevant transcription factors. These genes were screened by cis-acting element analysis, and the physical and chemical properties of the proteins were predicted. Our study provides a theoretical basis for the physiological and biochemical mechanisms and related key genes of exogenous MeJA in alleviating the CI of kiwifruit.