Embodiments of the present invention relate to a method and a system for controlling phase synchronization, and an apparatus. The method includes: determining a path from a non-reference base station to a preset reference base station, obtaining a first phase difference between every two adjacent base stations on the path, obtaining a second phase difference between the reference base station and the non-reference base station according to the first phase difference, and adjusting a non-reference phase of the non-reference base station to a reference phase of the reference base station according to the second phase difference. According to the method and system for controlling phase synchronization, and the apparatus that are provided in the embodiments of the present invention, in a single-frequency network system, phases of base stations are synchronized without a need to install a GPS antenna, so that system costs are reduced.