Esophagogastric junction cancer poses a great threat to human beings both in western countries and East Asia, especially in China and Japan, and its incidence has increased during recent decades. The 5-year survival rate of esophagogastric junction cancer is quite poor compared with that of other gastric cancer sites. Until now, the traditional TNM staging system has been widely used in clinical practice for prognosis. However, the TNM system is based on pathology after surgical resection or radiology using CT and MRI, not on blood markers. Evidently, some research has been reported concentrated on the prognostic value of blood-based markers with the character of non-invasive and non-radioactive in EJA. Hematologic, biochemical and coagulation parameters could be obtained from clinical data and utilized to analyze their prognostic values. Tumor-associated antigens, microRNAs and circulating tumor cells have also been reported in EJC prognosis. In this article, we review research focused on blood-based markers to evaluate their prognostic value in esophagogastric junction cancer, especially its main subtype adenocarcinoma.