Excessive exploitation of the groundwater has resulted in obvious three-dimensional (3D) deformation features on the surface of the Beijing Plain. This paper, by combining Interferometric Synthetic Aperture Radar (InSAR) and Global Positioning System (GPS) technologies, has obtained time-series information of the 3D surface deformation in the Beijing Plain, analyzing its spatial distribution characteristics. On this basis, the relationship between different controlling factors with the 3D deformation of the surface has been analyzed as well. The following results are obtained: (1) From 2013 to 2018, the land subsidence, which generally showed the trend of slowing down, was mainly concentrated in the eastern, northern, and southern regions of Beijing Plain, with multiple subsidence centers. (2) Under the International Terrestrial Reference Frame 2005 (ITRF2005), the horizontal direction of all GPS points in the plain is basically the same, with the dominant movement direction being NE112.5°~NE113.8°. Under the Eurasian reference frame, the horizontal movement rate of GPS points significantly decreases. The movement rate and direction of each point are not characteristic of overall trend activity. (3) The distribution and extent of the 3D surface deformation in the Beijing Plain are controlled by the basement structure. Part of the subsided area corresponds to a Quaternary depression formed at the junction of active faults disrupting the area. Similarly, the distribution of horizontal deformation in the E-W and N-S directions of the plain is controlled by the regional basement structure comprising major faults bounding horizontal deformation. (4) Groundwater exploitation is the main cause of the 3D surface deformation in the Beijing Plain. The groundwater funnels of the second and third confined aquifer are in suitable agreement with the land subsidence. The horizontal movement in the Beijing Plain is either directed toward the center of the groundwater or the land subsidence funnel, and the deformation is directed from areas with higher to areas with lower groundwater levels.