According to the dynamic similarity theory, the scale model of a container crane structure was designed, and the length of each component (beam) was similar to the size of the prototype. However, it was difficult to strictly alter cross section thickness according to the same scale. This problem can be effectively solved using the method of cross section radius of inertia similar to design the scale model. A series of finite element time history analysis and seismic sharking table tests were carried out for the prototype finite element model and the scale model. The results showed that the experimental results were close to the calculation results. The maximum acceleration and strain were nearly at the same positions at the same time. This indicates that the response of the scale model can reflect the real structure subject to seismic load and thus verifies the design method, which provides a reference for model design and seismic experimental research.