Separating a reentry vehicle into warhead and body 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 body, whose radar cross section is larger, and ignore the warhead, which is the most important part of the reentry vehicle. However, the procedure is difficult to perform using standard tracking criteria. This study presents a novel tracking algorithm by integrating input estimation and modified probabilistic data association filter to solve this difficulty in a clear environment. The proposed algorithm with a new defined association probability in this filter provides a good tracking capability for the warhead ignoring the radar cross section. The simulation results indicate that the errors between the estimated and the warhead trajectories are reduced to a small interval in a short time. Therefore, the radar can produce a beam to illuminate to the right area and keep tracking the warhead all the way. In conclusion, this algorithm is worthy of further study and application.