To estimate a spacecraft trajectory, the observation satellite position should be calculated in advance. Through the simplified equation of motion based on the observation satellite for finishing the second order differential equation. By the MATLAB simulation interpolation operation with the existing list data, solution to satellite of three dimensional position in different moments. By the point wise intersection positioning method to estimating the trajectory of the spacecraft, the position and velocity of the spacecraft in a certain time will be obtained. And using simulated annealing for the mathematical model of a spacecraft trajectory and analyzing the rationality of the estimate.