In order to reduce the damage of underground structure caused by unreasonable anti- floating design, the design concept of the anti-seismic and fire protection engineering was introduced into anti-floating design. Based on the concept of anti-seismic fortification design and the working mechanism of anti-floating bolt, the three-level fortification design method for anti-floating bolt system of underground structures was proposed, and the implementation idea of the design method was clarified. And then the three-level fortification design method was imported into the anti-floating bolt system. The anti-floating bolt design was optimized based on the failure project of the anti-floating bolt on the basement of a certain office building. The results show that based on the failure mechanism of the anti-floating bolt system, the parameter values such as anchorage length, bolt pull-out capacity, and bolt spacing were determined for the three-level fortification design concept, which met design demand. It is concluded that the three-level fortification design method for anti-floating bolt system of underground structures provides a basis for the safety management of anti-floating bolt system.