LEO satellite formation configurations may get an in-track drift under the perturbation of atmosphere. The area-mass-ratio of the satellite directly influences the decrease of semi-major axis caused by the perturbation atmosphere, so the in-track drift can be controlled by the adjustment of the area-mass-ratio. Taking the drift distance of the formation center and the difference of the semi-major axes as the input, and the change of area-mass-ratio as the control, a fuzzy controller for in-track drift of formation configuration was studied. On the basis of the design of the input fuzzification and the fuzzy rules, the Mamdani inference was used in the fuzzy inference, followed with a centroidal defuzzification. The simulation indicates that the drift distance can be controlled within 20m, with the given condition. The method proves effective, even with the presence of initial errors.