Separating a reentry vehicle into warhead, main body, and debris is a conventional and efficient means of producing a huge decoy and increasing the kinetic energy of the warhead. This procedure causes the radar to track the main body and debris, which radar cross section are large, and ignore the warhead, is the most important part of the reentry vehicle. The warhead is difficult to identify after separation using standard tracking criteria. This study presents a novel tracking algorithm by integrating input estimation and modified probabilistic data association filter to identify warhead among objects separation from the reentry vehicle in a clear environment. The proposed algorithm provides a good tracking capability for the warhead ignoring the radar cross section. Simulation results reveal that the errors between the updated and warhead trajectories are reduced to a small interval in a short time. Therefore, the radar can generate a beam to illuminate the right area and keep tracking the warhead all the time. This algorithm is worthy of further study and application.