Coexistence of organ dysfunction has been regarded as a risk factor in the surgical treatment of digestive diseases. The aim of this study was to investigate the correlation between coexistence of organ dysfunction and post-operative outcome in patients with thoracic esophageal squamous cell carcinoma (SCC). One hundred and fifty-eight patients with SCC of the thoracic esophagus, who had been surgically treated were examined, including 37 cases associated with organ dysfunction. The proportion of post-operative complication in patients with organ dysfunction (32.4%, 12/37) was significantly higher than that in patients without organ dysfunction (15.7%, 19/121; p=0.025). The overall survival of patients with organ dysfunction was significantly more unfavorable than that of patients without organ dysfunction (p=0.031), and multivariate analysis demonstrated that coexistence of organ dysfunction (p=0.004), depth of tumors (p=0.012), lymph node metastasis (p=0.0003), blood vessel invasion (p=0.008) and the incidence of post-operative complications (p=0.026) were factors independently associated with worse overall survival of the patients with SCC of thoracic esophagus. Coexistence of organ dysfunction was found to be an independent indicator of worse overall survival in patients with SCC of the thoracic esophagus.