A method, an apparatus and a system for estimating channels are disclosed. A method for estimating channels includes: receiving downlink signals inclusive of reference signals from two or more Access Points (APs), where the relative frequency shift between reference signals sent by different APs is zero; and performing channel estimation according to the reference signals. Another method for estimating channels includes: receiving downlink signals inclusive of reference signals from two or more APs, where for a first AP and a second AP among the two or more APs, a specific time-frequency lattice in the downlink signals sent by the first AP includes no data signal, and the specific time-frequency lattice corresponds to a time-frequency lattice utilized by the second AP to send a reference signal; and performing channel estimation according to the reference signals. The technical solution disclosed herein eliminates the interference between the reference signal and the data signal, enables the UE to estimate the channel value between the UE and the cooperative APs accurately, and improves the UE performance.