For a drag-free satellite, one core technology required to achieve the mission requirements is drag-free control. The purpose of control is to offset the interference such as sunlight pressure, gravitational gradients of Earth and Moon, nonspherical perturbation, etc. Currently, the drag-free controller design is mainly aimed at the full frequency band. This will inevitably mix the control signal into the scientific measurement signal, thereby interfering with the processing of scientific data. Besides, the control at the full frequency band will increase fuel consumption. To solve the above problems, this article presented the controller design method for a drag-free satellite with scientific measurement constraints, which covers motion model establishing, coordinate axis decomposition, frequency separation control strategy formulation, H∞ mixed sensitivity controller design, controller stability analysis, and performance results.