With the rapid intensification and scaling up of aquaculture, issues such as water quality deterioration, pathogen proliferation, compromised immunity of aquatic animals, and frequent disease outbreaks caused by high-density farming have become increasingly prominent. Traditional antibiotic-based prevention and control approaches pose ecological and food safety risks, including drug residues, microbial imbalance, and excessive antibiotic resistance, making them inadequate for meeting the demands of green, antibiotic-free aquaculture. Bacillus velezensis, a novel functional probiotic characterized by strong stress resistance, excellent colonization ability, and comprehensive probiotic functions, achieves multiple benefits-including water quality regulation, disease prevention, and growth enhancement-through various mechanisms such as secreting antibacterial compounds, modulating aquatic microecology, improving intestinal structure, and boosting non-specific immunity. It serves as a core functional additive for antibiotic-free aquaculture. This article systematically elucidates the biological properties and probiotic mechanisms of Bacillus velezensis, focusing on its applications in purifying aquaculture water, promoting aquatic animal growth, enhancing immune resistance, and optimizing intestinal microbiota composition. It also identifies current technical challenges and limitations in strain application, industrial production, and practical use, while proposing targeted optimization strategies and future development directions to provide theoretical and technical support for the large-scale, standardized application of Bacillus velezensis in sustainable aquaculture.