The present invention discloses a channel estimation method and device in a multi-antenna system. The method includes: obtaining the original channel estimation value of each array element of an array antenna for each uplink user received by the antenna; converting them into a channel estimation matrix; dividing the channel estimation matrix into an amplitude matrix and a phase matrix; grouping the elements of each array element at the same tap location in the amplitude matrix together for signal transformation processing and performing transform domain noise reduction to the high-frequency portion of the obtained transform domain data; inversely transforming the noise-reduced data to a noise-reduced amplitude matrix; and combining the noise-reduced amplitude matrix with the phase matrix into a restored channel estimation matrix, wherein the amplitude of each channel estimation value of the restored channel estimation matrix has undertaken a multi-antenna transform domain noise reduction process.