In order to realize the variation of structural dynamic characterics due to neighbor structures in buildings, the surface structure is idealized as an equivalent single degree of freedom system with rigid base whose site consists of a single homogeneous layer. The dynamic characteristics of three-dimensional structure-soil-structure interaction system, including two identical structures, are investigated to identify the additional effects caused by the presence of a second structure. When comparing the data from the soil-structure system with only one structure and the structure-soil-structure system, two close natural frequencies with opposite phase modes are identified. Therefore, the term twin-frequency is proposed. Next, the value of twin-frequency varying with the frequency ratio of structure to soil is discussed. Meanwhile, the relative distance between two structures and the ratio of foundation width to soil thickness are covered. The data will be used to consider the coupling effects of soil on the dynamic characteristics of structure-soil-structure systems. Finally, a numerical case of seismic response of the structure-soil-structure system is calculated under traveling wave excitations. The numerical results indicate that the twin-frequencies cause beatings of the structures as well as ground motion.