The invention includes a system for eliminating interference of adjacent base station and method thereof. The method includes: performing packetization, interleaving and repetition to the initial datablock to generate a logic data block, performing permutation to the logic data block to generate a physical data block, and transmitting the physical data block; receiving the physical data block, performing inverse-permutation and de-interleaving to the physical data block to obtain the logic data block, performing separation and estimation to the physical channel of the target base station andadjacent base station through the leading symbol or the pilot frequency symbol, performing inverse- permutation and de-interleaving to the physical channel to obtain the channel, constructing the estimated logic channel matrix through the estimated logic channel, calculating the weight coefficient based on the estimated logic channel matrix, equalizing the logic data block by using the weight coefficient, to obtain the equalized logic data block, performing reduction to the equalized logic data block to obtain the initial data block. By adoption of the invention, the interference of adjacent base station in the communication system is eliminated, and reliability of the communication system is improved.