The invention discloses a method and a system for processing reference signal of channel state information, both capable of using different reference signal sequences between different antenna port groups and randomizing the carrier interference between the different antenna port groups according to the different reference signal sequences. The reference signal sequences of each different antenna port of channel information reference signal can be generated at the network side, and then respectively mapped to the corresponding time frequency source according to the set position; the receiving side is capable of receiving the channel information reference signal on the corresponding time frequency source according to the high-level signaling at the network side, and the reference signal sequence of channel information reference signal can be generated with the same method as generating the reference signal sequence of the antenna port of channel information reference signal at the network side, then the channel estimation of the channel information reference signal and the measurement of channel information are carried out according to the received actual signal value. Therefore, the carrier interference between different antenna ports in the same cell can be effectively reduced with the method and the system of the invention.