As a member of the city life lines, water towers are still widely used as an outdoor device to supply water. Study on the seismic performance of the water tower is of great significance because earthquakes often happen in China. Finite element methods, such as the ANSYS, are widely used as traditional structural dynamic analysis methods, but the calculation efficiency of the ANSYS is very low. In this paper, the transfer matrix method of multibody system (MS-TMM) was introduced to analyze the seismic performance of a water tower. Based on the example as a water tower, the calculation speed of the MS-TMM is much faster than the calculation speed of the ANSYS and the responses obtained by the MS-TMM are nearly equivalent to the responses obtained by the ANSYS. Evidently, the MS-TMM can satisfy the requirements of calculation efficiency and calculation accuracy in computing the responses of water towers during earthquakes.