Provided is a precoding matrix design method for a cooperative communication of multiple base stations in a multiple input multiple output (MIMO) communication system. A method of designing a precoding matrix in a base station of the MIMO communication system may include: determining whether to use a cooperative communication; verifying a cooperative base station when the cooperative communication is determined to be used; selecting a precoding matrix to be applied by a home base station and the cooperative base station; and requesting the home base station and the cooperative base station for the cooperative communication using the selected precoding matrix.