The technology of multiple independently targeted reentry vehicles(MITRV) of the ballistic missile is an important part of missile technology. The working proceed of MITRV was given according to its principle. To satisfy the request of fast reaction in modern weapon system, aiming at the model characteristic of MITRV trajectory, the parallel computing technology was advanced to improve the computing speed and the parallel computing model of MITRV was built. From the result in Linux environment, this method can significantly improve the trajectory computing speed and achieve a high accelerate rate.