This review summarizes the interactions between host immunity and intestinal microorganisms in fish, focusing on recent advances in zebrafish (Danio rerio). Fish gut contains a large number of microorganisms that play crucial roles in maintaining host intestinal and general health. The host immunity can sense and shape the intestinal microbiota, maintaining intestinal homeostasis, while intestinal commensal microbes regulate the host immunity, control the proliferation of pathogenic microorganisms, and ensure intestinal health. The review highlights the complex interactions between host immunity and intestinal microorganisms in fish, emphasizing the role of zebrafish as a model organism for studying these interactions. It discusses the mechanisms by which host immunity recognizes and regulates intestinal microbiota, and how intestinal microbes influence host immunity. The review also explores the potential of intestinal functional microorganisms in fish aquaculture, providing theoretical references for their development, application, and commercialization. Key findings include the role of pattern recognition receptors (PRRs) such as TLRs, NLRs, CLRs, and PGRPs in host immune recognition of gut microorganisms, and the impact of intestinal microbiota on host immunity and disease resistance. The review concludes that understanding these interactions is crucial for maintaining fish health and improving aquaculture practices.This review summarizes the interactions between host immunity and intestinal microorganisms in fish, focusing on recent advances in zebrafish (Danio rerio). Fish gut contains a large number of microorganisms that play crucial roles in maintaining host intestinal and general health. The host immunity can sense and shape the intestinal microbiota, maintaining intestinal homeostasis, while intestinal commensal microbes regulate the host immunity, control the proliferation of pathogenic microorganisms, and ensure intestinal health. The review highlights the complex interactions between host immunity and intestinal microorganisms in fish, emphasizing the role of zebrafish as a model organism for studying these interactions. It discusses the mechanisms by which host immunity recognizes and regulates intestinal microbiota, and how intestinal microbes influence host immunity. The review also explores the potential of intestinal functional microorganisms in fish aquaculture, providing theoretical references for their development, application, and commercialization. Key findings include the role of pattern recognition receptors (PRRs) such as TLRs, NLRs, CLRs, and PGRPs in host immune recognition of gut microorganisms, and the impact of intestinal microbiota on host immunity and disease resistance. The review concludes that understanding these interactions is crucial for maintaining fish health and improving aquaculture practices.