A method for designing the nonlinear feedback control law is proposed in this paper for the electromagnetic formation flying system of fractionated spacecraft in low Earth orbit. Firstly, the magnetic force model and the Earth's magnetic field model are established, respectively. The effects of the Earth's magnetic field on the electromagnetic formation flying system in low Earth orbits are analyzed. Secondly, the high precision relative orbit dynamics model is presented. Then, a nonlinear feedback control law for relative orbit is proposed based on the Lyapunov's stability theorem. Finally, two fractionated modules electromagnetic formation maintenance scenario is simulated. The simulation results show that the magnetic disturbance force can be ignored; but the disturbance torque cannot be ignored. Furthermore, the fractionated spacecraft electromagnetic formation flying is fully controllable and the approaches proposed are feasible.