The incidence and mortality of esophageal cancer are high, with strong invasiveness and poor prognosis. In China, the number of morbidity and death accounts for about half of the world. The cause of the disease has not yet been clarified, and it is known to be related to many factors such as chronic damage to the upper digestive tract caused by poor diet and lifestyle, heredity and environment. With the continuous advancement of molecular biology technology, metagenomics and high-throughput sequencing began to be used as non-culture methods instead of traditional culture methods for micro-ecological analysis, and is becoming a research hotspot. Many studies have shown that the disturbance of upper digestive tract microecology may be one of the causes of esophageal cancer, which affects the occurrence and development of esophageal cancer through complex interactions with the body and various mechanisms. This paper reviews the research progress, which is of great significance to further clarify the value of upper gastrointestinal microecology in the pathogenesis, diagnosis and treatment of esophageal cancer.