A method and apparatus for controlling a handover in a cognitive radio system are used to control a cell handover process of a user equipment, and can hand over the user equipment to an appropriate target cell as far as possible. The method includes: a source base station receiving a measurement report send by a user equipment; the source base station controlling a handover of the user equipment according to the measurement report, radio resource management information, and reconfiguration related information. The apparatus is located in the source base station and includes a receiving module and a handover controlling module.