Germ-free models and bacterial transplantation technology facilitate the mechanism study of the host-gut microbe interaction. Among them, zebrafish is an economical and practical model with its characteristics, such as transparent larva and efficient gene manipulation, differing from the mouse. Here we enumerate the similarities and differences of the genes, the digestive tract structure and the gut microbiota of zebrafish and humans. And the recent reports on colonizing human gut microbes to zebrafish are elaborated. We summarize the advantages and limitations of this model and revalidate those with some important discoveries on the utilization of zebrafish in modeling human gut microbe research. This review will make the readers clear the advances in the application of zebrafish in gut microbiota-related researches.