In space attack-defense system, relative position and velocity estimation between intercepting satellite and target satellite is very important for orbit designing of intercepting satellite. In this paper, relative navigation is researched under the condition that orbit of target satellite is elliptical orbit and that the intercepting satellite has orbit maneuvering. Firstly, relative motion equations are derived with elliptical orbit of target satellite, and measurement equations are developed according to the geometric relation of measurement. Then the accelera-tion of intercepting satellite is introduced with its error, and the improved EKF algorithm is designed to increase navigation accuracy. Finally, the numerical simulation results verify the validity of this navigation method and show higher navigation accuracy.