The accurate measurement of the attitude of the ballistic correction projectile is the precondition for accurate correction. In order to solve the measurement accuracy problem of the strapdown-connected projectile magnetic sensor, the eddy current magnetic field is considered on the basis of the traditional error compensation model. A simplified mathematical model of the eddy current magnetic field of the pure rolling projectile was established, and the influence of the eddy current magnetic field interference on the magnetic measurement at different rotational speeds was simulated and analyzed. Aiming at the necessity of eddy current magnetic field compensation, a parameter estimation method of the non-independent attitude comprehensive compensation model based on Kalman filter algorithm is proposed. The normalized evaluation of the magnetic correction effect shows that the error of the parameter estimation result does not exceed 0.01%, and the magnetic measurement error after compensation converges to 0.19nT. The compensation effect is obvious and meets the laboratory magnetic measurement compensation requirements.