Abstract: Gut microbial "dark matter" refers to the microorganism that exists in low or rare abundance in the gastrointestinal tract and affects human health, without a clear disclosure of its influence and the related mechanism. Most current studies on the relationship among diet, gut microbiota, and host health have focused on the high-abundance gut microbiota, while the role of gut microbial "dark matter" has often been neglected. Therefore, this paper reviews the interactions among dietary nutrition, gut microbial "dark matter", and host health, as well as the new advances in microbiomics technologies, discusses the importance of exploring the acting mechanisms of microbial "dark matter" on human health, and provides new ideas for future dietary interventions to influence gut microbiota for preventing or even improving human diseases.