Methylation levels are inversely associated with gene expression in classical epigenetic regulation. Overexpression of long non-coding RNA (lncRNA) ESCCAL-1 promotes esophageal squamous cell carcinoma (ESCC) malignancy. It is not unknown whether the mRNA expression of the ESCCAL-1 promoter can be inhibited by targeted editing of its methylation levels to inhibit the malignancy of ESCC. In this study, we first confirmed the hypomethylation status of the ESCCAL-1 promoter by methylation sequencing and chose appropriate regions for methylation editing. We successfully established the clustered regularly interspersed short palindromic repeats/CRISPR-associated nuclease 9 (CRISPR/Cas9)-Dnmt3a plasmid system that can edit the methylation levels of the ESCCAL-1 promoter and confirmed its function to restore the methylation levels of the ESCCAL-1 promoter. We found that the constructed plasmid system can reduce the malignancy of ESCC by inhibiting the expression of ESCCAL-1 mRNA in vivo and in vitro. Further study of the mechanism revealed a new regulatory pathway that restored the methylation of the ESCCAL-1 promoter and promoted the autophagy and apoptosis of ESCC by inhibiting the activation of the PI3K/Akt signaling pathway. These findings suggest that editing the methylation of ESCCAL-1 promoter can be a novel therapeutic approach to treat ESCC.