The embodiments of the present invention provide a method for configuring a reference signal, a base station and a user equipment. The method includes: receiving, by a first base station, candidate reference signal configuration information of a second base station transmitted by the second base station, and/or candidate reference signal configuration information of the first base station transmitted by an operation and maintenance entity (OAM); and configuring, by the first base station, a reference signal for a user equipment (UE) according to the candidate reference signal configuration information of the second base station, and/or, configuring, by the first base station, a reference signal for a UE according to the candidate reference signal configuration information of the first base station.