Aeromagnetic compensation accuracy is one of the key factors affecting the accuracy of geomagnetic navigation. A component compensation method is proposed based on improved Fuzzy Adaptive Kalman Filtering. The observation matrix in Kalman filter is modified to effectively improve the low speed convergence. By monitoring the variance ratio between the residual output and theoretical residual at each moment, the measurement noise covariance is modified step by step and the optimal parameters are obtained. Simulation results show that this presented method has strong adaptability to timevarying measurement noise. The total field compensation error is reduced from 175.8 to 6.7 nT, component error is reduced from 59.2, 110.2, 122.2 nT to 6.0, 1.7, 1.5 nT, respectively. Experiment is carried out by constructing a vector system and its results demonstrate that the proposed method performs better in convergence speed and compensation accuracy. The proposed method can provide a good reference to distortion magnetic field compensation.