A method and apparatus of configuring a multi-cell precoding matrix for a multiple input multiple output (MIMO) operation in a wireless communication system in which a plurality of base stations participate in cooperative communication is provided. A multi-cell precoding matrix is configured using one or more single-cell precoding matrices, and wherein coefficients to be multiplied by the single-cell precoding matrices satisfy a condition in which the product between the multi-cell precoding matrix and a Hermitian matrix of the multi-cell precoding matrix is a unitary matrix. According to the embodiment of the present invention, it is not necessary for all base stations to perfectly know channel information. In addition, a feedback overhead is not high, and complexity is low.