Traditional Chinese fermented foods, usually produced through fermentation by spontaneously inoculation, are characterized by their special flavors and rich nutrients. The techniques of some traditional fermented foods have thousands of years of history. In recent years, new technologies have been used to explore the mysteries of fermenting processes for traditional fermented foods worldwide, revealing that traditional fermentation systems are valuable to both basic and application research. In this review, we summarize the general features and recent progresses in the microbiome study of traditional Chinese fermented foods, and try to predict the future research directions.