Pear fruits are usually harvested in the mid-summer and need to be stored at low temperatures to prevent deterioration and extend their shelf-life. However, low temperature induces lignin deposition and increases stone cell numbers, impairing fruit quality and decreasing consumer satisfaction. In this study, we found that postharvest application of MeJA could efficiently inhibit lignification in pear fruit 'Xinli No.7′ and 'Zaosu' under low-temperature storage (4 °C). Transcriptomic and metabolomic analyses indicated that MeJA application may inhibit lignin polymerization and aggregation by repressing the expression of genes encoding enzymes in the late stage of the lignin biosynthesis pathway. Also, MeJA may alleviate ROS-mediated lignification by promoting flavonoids accumulation. Moreover, the inhibition of the lignification process by MeJA likely depends on the activation of endogenous JA biosynthesis and its signaling pathway. Our findings shed light on the lignification process and the role of MeJA in its regulation in pear fruit under low-temperature storage, and provide a means of alleviating deleterious lignification during storage.