Salicylic acid (SA) is a natural phytohormone that can reduce chilling injury (CI) in fruit and vegetables. In this study, we used transcriptome analysis to investigate the effects of SA treatment on the low-temperature storage process in kiwifruit. Specifically, we compared the differences in the phenylpropane metabolic pathway and the phytohormone signaling pathway during low-temperature storage after SA treatment. Our results showed that SA treatment inhibited fruit softening, reduced respiration rate, and alleviated CI symptoms in kiwifruit. Additionally, transcriptome results indicated that SA treatment enhanced the gene expression and activity of enzymes related to phenolic syntheses, such as phenylalanine ammonia-lyase (PAL), cinnamic acid-4-hydroxylase (C4H), and 4-coumaric acid coenzyme A ligase (4CL), resulting in increased phenolic content. SA treatment may also alleviate CI by regulating the signal transduction pathways of key phytohormones, including gibberellin (GA), jasmonic acid (JA), SA, and abscisic acid (ABA), which can achieve growth inhibition and enhance stress response. SA response elements were identified in the promoter regions of many key differential genes. This study provides valuable insights into the molecular basis and key gene associated with the mechanism of SA in mitigating the CI of kiwifruit.