It has been discovered that intestinal fungi play important roles in microecological systems of human body, which affect the human health by influencing gut microbiota directly or indirectly. This article reviews the research progress about the fungi-bacteria interaction, and effects of intestinal fungi and their products on host’s health. The article also discusses the correlation of intestinal fungi with inflammatory bowel disease, colorectal cancer, HBV-related liver diseases, metabolism-associated fatty liver disease and alcoholic liver disease, indicating that intestinal fungi are widely involved in the development of human diseases.