Objective To analyze copy number variance (CNV) in whole genome by using gene chip technology, and to screen the radiosensitivity associated genes on esophageal squamous cell carcinoma (ESCC). Methods The patients with ESCC who received radiotherapy alone in Anyang Tumor Hospital from December 2013 to August 2016 were selected, and biopsy paraffin samples were preserved in the center of pathology. The patients were divided into radiosensitivity group (group S) and radio-resistance group (group R). DNA was extracted from these paraffin samples in both groups. Whole human genome CNV was detected by using genechip from OncoScan Array platform designed by Affymetrix company, and the differences of gene segments were screened in the two groups. Results Nineteen samples of ESCC patients were collected to extract DNA in this study. To balance pair analysis in the two groups, 10 samples were selected from the qualified patients, including 5 cases in group S and 5 cases in group R respectively. There were no statistical differences in gender, age, lesion site, lesion length, radiation dose of the two groups (all P> 0.05). Loss of heterozygosity (LOH) was the main type of CNV. The analysis results showed that LOH in q24.32-q24.33 of chromosome 10 and LOH in q21.2-q21.31 of chromosome 18 had high frequencies (100 ％) in group R, however, none were detected in group S. LOH in q27-q28.1 of chromosome 4 had a high frequency (80％) in group S , however, none were detected in group R. Conclusion LOH in 10q/18q is related to radio-resistance in ESCC, and LOH in 4p is associated with radiosensitivity in ESCC.