Magnetic anomaly detection based on magnetic gradient tensor has become more and more important in civil and military applications. Compared with methods based on magnetic total field or components measurement, magnetic gradient tensor has some unique advantages. Usually, a magnetic gradient tensor measurement array is constituted by four three-axis magnetometers. The prominent problem of magnetic gradient tensor measurement array is the misalignment of sensors. In order to measure the magnetic gradient tensor accurately, it is quite essential to calibrate the measurement array. The calibration method, which is proposed in this paper, is divided into two steps. In the first step, each sensor of the measurement array should be calibrated, whose error is mainly caused by constant biases, scale factor deviations and nonorthogonality of sensor axes. The error of measurement array is mainly caused by the misalignment of sensors, so that triplets’ deviation in sensors array coordinates is calibrated in the second step. In order to verify the effectiveness of the proposed method, simulation was taken and the result shows that the proposed method improves the measurement accuracy of magnetic gradient tensor greatly.