The problem of multi-target tracking by double-satellite cooperative detecting is studied. Firstly, the observability is analyzed according to the detecting geometry of two satellites. And the state equations and measurement equations of powered phase are established according to the turning model based on gravity. Secondly, to solve the problem of flight path tracking abnormity in the situation of multi-target tracking, an SME filter algorithm based on binary polynomial, called BPGM-SME, is put forward. In order to improve the accuracy and convergence rate of single-target tracking, an improved UKF algorithm based on iteration is given. Finally, the simulation indicates that: 1) The BPGM-SME algorithm has fine tracking performance for multi-target tracking;and 2) In single-target tracking, the improved UKF has better convergence effect and tracking accuracy than that of the original UKF.