In recent years, more and more studies have shown that intestinal flora is critical to the development and progression of metabolic-related fatty liver disease (MAFLD). This article summarizes MAFLD-related intestinal flora and metabolites and their possible mechanisms of action in disease process. Although related intestinal flora and metabolites are expected to become new noninvasive diagnostic markers and therapeutic targets for MAFLD, their clinical application still requires more in-depth research. The development of modern high-throughput sequencing technology provides new ideas for research. The integrated analysis of multi-omics, such as genes, proteins, transcription, and metabolism, allows us to establish a comprehensive understanding of the microbial factors affecting MAFLD under the precision medicine system, so as to lay a foundation for targeted transplantation of intestinal flora and drug development for liver metabolic homeostasis.