High susceptibility of mangoes to low temperature leads to ripening failure that restricts the marketability of products. This study investigated the effect of methyl jasmonate (MeJA) on ripening disorder and mechanism involved in mangoes during refrigeration. Results showed that 50 μM MeJA ameliorated ripening disorder, as indicated by accelerated advancement of ripening-related parameters. Transcriptome analysis revealed that 17,414 significantly differentially expressed genes were mainly enriched in ethylene synthesis, cell wall degradation, starch degradation and sugar transport. Moreover, 8 AP2/ERF transcription factors and 12 ripening-related genes were characterized via qRT-PCR. Afterwards, through the analysis of transcription factor binding sites and cis-acting elements, a regulatory network of ERFs mediated alleviation of ripening disorder conferred by MeJA was constructed. Finally, the interactions between MiERFs and the promoters of target genes were verified by yeast one-hybrid assay. Our findings provide a theoretical basis for improving cold tolerance via counteracting ripening disorder in mangoes.