Embodiments of the present invention disclose a method, an apparatus, and a system for processing a reference signal. The present invention relates to the field of radio communications technologies, and solves a technical problem that it is impossible to meet a requirement for measurement of downlink channels of multiple cells in a coordinated multipoint transmission/reception (CoMP) scenario in the prior art. According to the embodiments of the present invention, a reference signal is sent in a specified pilot position to a target user equipment (UE) where data puncturing is performed, in positions corresponding to the specified pilot position, with respect to data symbols simultaneously sent by an evolved NodeB (eNB) to which another cell in a CoMP set of the UE belongs, and the specified pilot position is orthogonally separated from a reference signal pilot position of the another cell in the CoMP set.