Objective: This study aimed to screen the potential molecular targets for proximal, mid, and distal esophageal cancers.Methods: The clinical data, RNA-seq data, and survival data for TCGA esophageal cancer were retrieved from UCSC Xena database. The samples with clinical information on the esophageal tumor central location were selected. Differential analyses on different groups (mid vs. proximal, distal vs. proximal, and distal vs. mid) were performed. Following the differentially expressed genes (DEGs) in three groups were analyzed, the common genes were subjected to survival analysis, miRNA prediction, and drug-gene analysis. The specific genes were annotated for functional and module analyses.Results: Six common genes, namely KCNA1, CCDC196, UNC5CL, CYP3A5, CA10, and REG3A, were analyzed among three comparison groups. The expression of CA10 and REG3A was significantly correlated in the prognosis of patients with esophageal cancer. The distal vs. mid groups screened 766 specific DEGs, and the mid vs. proximal group screened 99 specific DEGs. Functional analysis showed that the genes of distal vs. mid groups, including EDN3, CGA, CCR9, and GABRA2, as well as genes in the mid vs. proximal groups, including GCGR, OXTR, and MCHR2, were significantly enriched in neural functions. In the distal vs. proximal groups, there were 314 specific DEGs, including CYP2C8 and OXGR1.Conclusion: Six common genes may serve as the potential molecular targets for the treatment of all proximal, mid, and distal esophageal cancers.