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 earthquake resistance and the working mechanism of anti-floating anchor, the three-level protection design method for anti-floating anchor system of underground structure was proposed, and the implementation idea of the design method was clarified. The three-level protection design method of the anti-floating anchor system in underground structure was utilized to study the optimization scheme for anti-floating anchor design, using a case study of the failure engineering of anti-floating anchors in the underground basement of a specific office building. This research determined parameters such as anchor fastening item length, anchor pull-up bearing capacity, and anchor spacing under the concept of three-level protection design. The results were verified by combining them with the failure engineering of the office building's underground basement. The findings indicate that both local and overall anti-floating design calculations, as well as stability calculations for atrium anchors and shear calculations at column base joints within the atrium range and at bottom slab-isolated base junctions, all meet design requirements. It is concluded that the three-level protection design method for anti-floating bolt system of underground structures provides a basis for the safety management of anti-floating bolt system.