A method for processing in-device coexistence configuration information, apparatus and system. The method includes: notifying, by a source base station to a target base station, first in-device coexistence configuration information configured by the source base station for terminal equipment, when handover from the source base station to the target base station occurs in the terminal equipment. In this way, the source base station may notify the first in-device coexistence configuration information configured by it for the terminal equipment to the target base station; the target base station receives the first in-device coexistence configuration information, determines whether to configure the terminal equipment with in-device coexistence configuration information, and then notifies the source base station of related configuration information via a handover command. Wherein, when handover occurs in the terminal equipment, the in-device coexistence configuration information may be processed effectively.