With the development of high-throughput sequencing and omics technology, more and more studies have been conducted on the correlation between human microorganisms and diseases. The occurrence and development of many diseases have a great relationship with the imbalance of human microorganisms. And it can even be used as a tool for early diagnosis. However, a large number of experiments are needed to confirm the association between head and neck malignant tumors (HNMT) and imbalance of microorganisms. This paper reviews and summarizes the research progress of the disorder between HNMT and human microorganism. The aim is to find an early diagnosis method for HNMT so as to achieve timely prevention, early diagnosis and early treatment. It will help to continue to explore the relationship between human microorganisms and HNMT in the future.