A multi-cell coordination system and a channel calibration method thereof are provided. A reference apparatus receives a beam-precoding downlink reference signal via a directional beam from a base station. The base station receives a beam-precoding uplink reference signal via the directional beam from the reference apparatus. The server receives uplink and downlink channel information, where the uplink channel information is generated based on the uplink reference signal, and the downlink channel information is generated based on the downlink reference signal. The server obtains a channel calibration coefficient according to the uplink and downlink channel information. The channel calibration coefficient is used for estimating a downlink channel. Accordingly, the problem of conventional coordination system can be solved, and the embodiment can be implemented in multi-beam base station.