The invention provides a center line deviation rectifying method for a ballastless track of a high-speed railway of a roadbed segment. The method includes the following steps that the center line deviation amount and settling amount of a ballastless track line are measured; measured data are analyzed, and in combination of the track structure characteristics, lifting points and jacking points are arranged at the lower portion and the side face of a whole roadbed of a ballastless track structure; lifting devices are installed on the lifting points, the whole roadbed of the ballastless track and an upper structure are finely lifted, after an interface between the whole roadbed and graded gravel is jacked to be loosened, the lifting devices are unloaded, and the whole roadbed falls back; jacking devices are installed on the jacking points, and through grouped loading and level-by-level jacking, the ballastless track line is rectified to a designed position; and after line center line deviation rectification is finished, line restoration operation is conducted, a gap in the lower portion of the whole roadbed of the ballastless track is filled with polymer cement mortar, and line smoothness is restored through a fine adjustment fastener system. By the adoption of the method, the problem of center line deviation of the ballastless track line of the roadbed segment can be safely, rapidly and effectively solved within a skylight time, and line smoothness is restored.