The rise of intensive aquaculture in recent year has led to frequent occurrence of fish diseases, with the increased morbidity and mortality in juvenile fish posing a particularly serious threat to the development of the industry. Accordingly, how to protect the health of juvenile fish has become an urgent problem for the development of aquaculture. Probiotics can promote the growth and development of juvenile fish by resisting pathogens and water pollutants, promoting the uptake of nutrients, regulating the immune system, modulating intestinal microorganisms, and enhancing intestinal barrier of juvenile fish. However, the mechanisms related to such processes still require further exploration. This review summarizes the beneficial effects of probiotics on juvenile fish development and their possible mechanisms. We also address the challenge of the probiotics in juvenile fish farming, which may provide valuable information for the application of probiotics in juvenile aquaculture.