Electromagnetic formation flight uses the electromagnetic interaction between satellites to provide maneuver control for formation satellites, with the advantages of no propellant consumption, long life, and high flexibility. However, high-precision control for electromagnetic formation flight is challenging because of the nonlinear and coupling characteristics of the dynamics, optimal assignment of magnetic dipoles, model uncertainties, and the angular momentum management issues caused by the geomagnetic field. This paper studies the 6-DOF control problem of two-satellite electromagnetic formation flight in low-Earth orbit. A new electromagnetic frame is introduced to promote the decoupling of the translation dynamics model and the electromagnetic model. The electromagnetic model can be expressed as a simple two-dimensional model in this electromagnetic frame. The proposed electromagnetic force envelope diagram can intuitively show the relationship between electromagnetic force and magnetic dipoles, providing practical guidance for dipole assignment. The frequency division multiplexing method is designed for angular momentum management considering the effect of the earth’s magnetic field on the electromagnetic satellites, and the active disturbance rejection control method is used to solve the 6-DOF stability problem with external disturbance and model uncertainties. Numerical simulation verifies the effectiveness of the proposed control method and angular momentum management strategy.