The present invention provides a method and an apparatus for processing network configuration, and a radio network controller. The method includes: establishing a neighboring cell relationship between a macro cell and a generic access network cell, where the neighboring cell relationship is a neighboring cell mapping relationship between a radio network controller of the macro cell and a generic access network controller of the generic access network cell, and more than two generic access network cells share one generic access network controller; and when a handover of a user equipment from the macro cell to the generic access network cell occurs, sending a measurement control message to the user equipment according to the neighboring cell relationship between the macro cell and the generic access network cell.