The invention discloses a magnetometer correction method based on ellipsoid fitting. The method comprises the following steps: 1, establishing a magnetometer error model according to the influence ona magnetometer by error; 2, converting the magnetometer error model into a magnetometer ellipsoid error model according to collected magnetometer measured data; 3, calculating parameters in the magnetometer ellipsoid error model, and working out ellipsoid fitting residual; 4, determining a satisfaction interval, and calculating satisfaction value and a satisfaction interval probability, removing denoising points when the satisfaction interval probability is smaller than the satisfaction value, returning the step 3, recalculating the parameters in the magnetometer ellipsoid error model throughremaining data, working out the ellipsoid fitting residual, re-executing the step 4 till the satisfaction interval probability is greater than the satisfaction value, and further working out the ellipsoid fitting error, so as to accomplish magnetometer correction. The method can effectively improve magnetometer correction and compensation precision, and is high in reliability, low in cost, high inprecision and simple in calculation process.