This paper describes the research on the pseudorange positioning of Autonomous Formation Flyer (AFF) of two satellites using pseudolites onboard, which is proposed by the NASA's Space Technology (ST-3). We build model and resolve relative position and time bias between satellites using Cartesian coordinate. The solution error covariance is very grave and unstable because observation geometry is very weak. In order to resolve this problem, we change Cartesian coordinate into sphere coordinate. It can be found that in the sphere coordinate system the solution error covariance is stable and can be used for simulation/covariance analysis.