High flux reactor is an important engineering test reactor, which can be used in irradiation research of materials, chemistry, isotopes, medicine and other fields. In the high flux reactor coolant system, there are a large number of nuclear pipes and the layout is complex. The optimization of seismic analysis method for reactor coolant system is an important part in the design process to ensure the nuclear pipes meet the design specifications. The traditional single point response spectrum method needs to envelope the response spectrum of different floors as the analysis input. This method is difficult to give the reasonable seismic load to the numerous nuclear pipes and it will increase the design cost and the difficulty of safety analysis about nuclear pipe. In this paper, an optimized seismic analysis method of reactor coolant system is proposed. By using the multi-point response spectrum method, the optimization of different excitation loading modes for different constrained support points is realized. The analysis results show that the multi-point response spectrum method can solve the problem that different support points are located at different elevation floors in the reactor coolant system, which makes the calculation results more accurate and reasonable. Compared with the traditional method, it can make the design more efficient and practical.