A blind adaptive channel mismatch equalisation method for global navigation satellite system (GNSS) antenna arrays is proposed. The anti-jamming performance of the antenna arrays is limited by the channel mismatch that is a relative characteristic of each radio frequency channel but not an absolute non-ideal characteristic. To pre-process the received data in the frequency domain, the least mean square (LMS) algorithm is used. The reference signal in LMS is the received data in the reference element. The purpose of pre-processing is to make the received data in the other elements approach the reference signal, which, in essence, is to equalise the mismatched channel. Without any auxiliary sensors and calibration source, this method can estimate the channel characteristics relative to the reference elements. Simulations and experimental results show that the proposed method is significant in improving the anti-jamming performance.