At present, complex super high-rise buildings and super high-rise buildings are emerging all over China, but there are still many problems to be solved in the design of super high-rise structures. For example, the wind pressure and earthquake risk of high-rise buildings, fire safety issues and personnel evacuation issues, earthquake will produce greater inertia force and bending force in high-rise buildings, wind load and wind pressure effect will be more significant, these are the parts that need to be carefully considered to ensure the safety and stability of the building structure. Therefore, it is necessary to analyze and optimize the problem of high-rise buildings. Taking a super high-rise building in Luohu District of Shenzhen City as an example, this paper analyzes the basic structure of super high-rise building, analyzes the key problems of structural design, and discusses the optimization method. This paper puts forward the optimization design method of building structure for seismic problem of super high-rise building structure, puts forward the solution to wind resistance problem, and puts forward the optimization layout method of building fire protection.