The use of different Rayleigh damping coefficients in the seismic response analyses of large quayside container cranes will generate very different results. By taking into account factors such as the boundary constraints of the container cranes, with reference to the method commonly used in engineering for calculating Rayleigh damping coefficients, we improve the method for calculating the damping coefficient and the frequency selection method for container crane structures based on a comparative analysis of similar model-test data and simulation results. Using the simulation method and shaking table tests, we compare and analyze the dynamic responses of the container crane structure under different Rayleigh damping coefficients. The results show that the influence of the methods used to calculate the Rayleigh damping coefficient and to select the frequency on the seismic response of the container crane structure increases with increases in the strength of the earthquake. When the peak acceleration is 0.4g or 0.62g, the average error between the simulation result and the test value obtained by the existing damping-coefficient calculation method exceeds 20%, whereas the error between them is within 10% when using the improved damping-coefficient calculation method.