Modern high-intensity aquaculture has seen a rapid increase in annual cultured production over recent decades, and it is essential to deal with the amount of waste produced. Aquaculture effluent is typically characterized by increased nitrogen species (ammonia, nitrites and nitrates), organic carbon, phosphates, suspended solids, and high biological oxygen demand and chemical oxygen demand. Probiotics are defined as live microbial or cultured product feed supplements that beneficially affect water quality or the host. For example, some strains can degrade ammonia, nitrites or nitrates and are important for water manipulation in intensive aquaculture. As a result, the use of probiotics in aquaculture is gaining increasing scientific and commercial interest worldwide. A strain with high protease activity, which can degrade protein or nitrogen, is key to its commercial application in probiotics production. To breed a B. subtilis BC2) was mutated using different doses of ultraviolet (UV) radiation, and a preliminary study determined the optimal UV radiation conditions. The value of flat transparent circle to colony diameter (. The results showed that the value of mutated strain B38 increased from 3.01 to 6.42. A spectrophotometry method with Forint phenol (Lowry) was used to measure the protease activity of the mutated strain. The protease activity of B38 was 86.82 U/mL, which was increased by 3.14 times compared with the original strain. After ten successive generations, the protease activity of B38 was 77.01 U/mL and did not change significantly, showing its good genetic stability. Cellulase activity analysis was used to determine whether the UV mutagenesis also affected other enzyme activity. The result showed that the cellulase activity of B38 was not significantly different from BC2. Subsequently, we evaluated the ability of mutated strain B38 to degrade feed protein. Protein content in the feed medium was assayed by the Kjeldahl method. The liquid protein degradation ability of B38 was an increase of 2.57 times compared with original strain BC2. However, the ability of B38 to degrade solid protein did not increase significantly. The UV-mutated high protease-producing B38 strain provides an important foundation for the development and application of aquatic probiotics.