Esophageal basaloid squamous cell carcinoma (bSCC) is a subtype of squamous cell carcinoma (SCC) with different behavior and poor prognosis. Exploring bSCC's molecular characteristics and treatment strategies are of great clinical significance. We performed multi-omics analysis of paired bSCC and common SCC (cSCC) using Whole Exome Sequencing and a NanoString nCounter gene expression panel. Immunohistochemistry was used for verification of candidate biomarkers. Different treatment response was analyzed on both patients receiving neoadjuvant treatment and on late-stage patients. The common genetically-clonal origin of bSCC and cSCC was confirmed. No significant differences between their genetic alterations or mutation spectra were observed. Mutation signature 15 (associated with defective DNA damage repair) was less prominent, and TMB was lower in bSCC. bSCC with RNA expression pattern resembling cSCC had better survival than other bSCC. Moreover, bSCC showed significant upregulation of expression of genes associated with angiogenesis response, basement membranes, epithelial-mesenchymal transition, and downregulation of KRT14 (squamous differentiation) and of CCL21 (associated with immune response). Immunohistochemistry for SFRP1 was shown to be highly sensitive and specific for bSCC diagnosis (p<0.001). In addition, bSCC receiving neoadjuvant immuno-chemotherapy had worse pathological response than neoadjuvant chemotherapy (but without statistical significance), even in bSCC positive for PD-L1. Our results demonstrated the molecular characteristics of esophageal bSCC as a subtype with distinct RNA expression pattern and immune characteristics, but no specific genetic mutations. We provided a useful biomarker, SFRP1, for diagnosis. With outcome analysis for 6 bSCCs with neoadjuvant immunotherapy treatment and 4 late-stage bSCCs with immunotherapy, we found that immunotherapy may not be an effective treatment option for most bSCC. This may also provide a clue for the same subtypes of lung and head and neck cancer. Our study highlighted the heterogeneity among bSCC patients, and might explained the conflicting results of bSCC outcomes in existing studies. This article is protected by copyright. All rights reserved.This article is protected by copyright. All rights reserved.