Significant rocking behavior appears in three-dimensional （3D） base isolated structures under earthquake ground motions and it affects the isolation effect of the 3D isolation technology. Different types of earthquake ground motions result in different influence effects to the rocking performance of 3D base isolated structures. 1567 earthquake ground motions with different characteristics are selected and classified. A method to evaluate the rocking performance of 3D base isolated structures is proposed based on the ratio of the vertical and horizontal acceleration response spectrum values and it is verified by finite element method. The influences of different focal mechanism， epicenter distance and site type on the rocking performance of 3D isolated structure are analyzed. The results show that the influences of different focal mechanism， epicenter distance and site type on the rocking of three-dimensional isolated structure are significant. Different types of earthquake ground motions are adjusted to have the same vertical acceleration response of the structures. In the typical isolation range （i.e.，2.0~5.0 s for horizontal isolation， and 0.3~1.0 s for vertical isolation）， the rocking angle of the 3D isolated structure is larger under reverse fault and strike slip fault earthquakes than that under normal fault earthquakes. It is larger under far-field earthquakes than that under near-field earthquakes， and it is generally larger under the earthquakes in soft soil site than that in hard soil site.