A flexible structure and design method for rocket engine thrust fidelity measurement are provided. The flexible structure comprises an upper body of an elongated cylindrical structure, the lower end of the upper body is connected with the upper end of a transitional body; the transitional body is of a structure similar to a half spheroid; the lower end of the transitional body is connected with the upper end of the weak body; the weak body is a rotary structure formed by rotation of two circular arcs around the axis; the lower end of the weak body is connected with the top of the lower body; the lower body is a flat cylinder structure; the upper body, the transitional body, the weak body and the lower body are integrally cut and formed. The design method is to analyze the engineering situation and define the stress condition and boundary condition. Then the topology reduction optimization is carried out to determine the initial shape of the flexible structure and the topology reductionoptimization is carried out. Repeated iteration is performed to achieve the ideal value; then the three-dimensional structure is designed on the basis of two-dimensional images. The three-dimensionalfinite element simulation analysis is carried out; whether the structure is reasonable or not is judged and the structure is finally output. The flexible structure of the invention has less influenceon the force transmission effect, so that the experiment result is more accurate.