To investigate the isolation effect of the friction pendulum system (FPS) horizontal isolation bearing and the air spring‐FPS three‐dimensional (3D) isolation bearing in truss structure and the influences of long‐period ground motions on the isolated structure, the shaking table test of a truss structure is designed and conducted. The ordinary ground motions, near‐fault pulse‐like ground motions, and far‐field long‐period ground motions with different spectral characteristics are chosen to input into the structure, and the dynamic characteristics such as the acceleration, displacement, and stress of the truss are compared and analyzed. The horizontal frequency of the horizontal isolated structure is reduced after the horizontal isolation, while the vertical frequency is further reduced after 3D isolation. The isolation effect of nodal acceleration, nodal displacement, and member stress under 3D isolation is better than that of horizontal isolation, especially the vertical seismic response is significantly improved. When the ground motion intensity is small, the FPS horizontal isolation bearing slides little, and reducing the seismic response of the structure is limited. There is a better isolation effect of 3D isolated structure. The vertical frequency ratio Rf under ordinary ground motions is far away from 1 and close to 3, basically avoiding the main energy segment of the ground motions. The advantage of 3D isolated structure is relatively reduced under long‐period ground motions, which lies in the rich low‐frequency components of long‐period ground motions which are difficult to isolate effectively.