The Alzhai Grottoes are challenged by a saline-alkali environment that causes the murals to crumble and peel. Traditional restoration methods are not effective in this environment and can lead to secondary damage. This study employs microbial-induced calcium carbonate precipitation (MICP) technology, using specific bacteria to induce mineral deposition under saline-alkali conditions, forming a protective mineralized layer. The study isolated and screened a mineralized strain, Bacillus oceanicum, which was compared to the traditional mineralizing bacterium Pasteurella. Laboratory experiments revealed that Bacillus oceanicum exhibited higher solidification strength, uniform solidification, and better salt-alkali tolerance. The cohesion of specimens treated with Bacillus oceanicus increased by 83.18%, and the internal friction angle increased by 29.06% compared to Bacillus pasteurii-treated specimens. The study demonstrated that Bacillus oceanicum effectively treated the saline-alkali diseases in the Alzhai Caves’ murals, reducing the height of phthalate, the volume of crisp powder, and the thickness of salt crust in MICP-treated samples by 29.1%, 45.0%, and 36.4%, respectively, compared to untreated specimens. This research provides new insights and methods for the protection and restoration of cultural relics in special environments, focusing on the green microbial technology for disease control and preventive protection of murals.