Ellipse fitting is a useful tool to obtain the differential signal of two atom interference gravimeters. The quality stan-dard of ellipse fitting should be the deviation between the true phase and the fitting phase of the interference fringe. In this paper, we present a new algorithm to fit the ellipse. The algorithm is to minimize the differential noise of two interference gravimeters and obtain a more accurate value of the gravity gradient. We have theoretically derived the expression of the differential-mode noise and implemented the ellipse fitting in the program. This new algorithm is also compared with the classical methods.