Microbial-Induced Calcium Carbonate Precipitation (MICP) is an environmentally friendly, efficient, and sustainable new soil reinforcement technology. For this study, Bacillus pasteurii were domesticated and cultured in a natural seawater environment with multiple gradients and used for coral reef calcareous sand reinforcement, comparing the mineral composition of the generated precipitates and the reinforcement strength under different domestication gradient conditions. The results revealed that, while the natural seawater environment inhibits the growth of Bacillus pasteurii, the gradient domestication method allows the bacteria to gradually adapt to the natural seawater environment. Notably, their shape becomes thin and long under the seawater environment. Furthermore, the MICP mineralisation reaction rate is faster in the natural seawater environment and, with an increase in the domestication gradient, the mineralisation reaction precipitates increased. At the same time, in the seawater environment, a small amount of mineral components were generated in addition to CaCO3, such as MgxCay(CO3)z, and the Mg2+ mineral content increased with an increase in the domestication gradient. When comparing the curing effect under different gradients in the natural seawater environment, it was found that the Bacillus pasteurii can effectively enhance the curing effect of the calcareous sand after multi-gradient domestication in the seawater environment, with the curing effect increasing with an increase in the domestication gradient. The results of this study provide new ideas for the application of MICP technology in seawater environments for the reinforcement of calcareous sand in the construction of South China Sea islands and reefs.