As nanotechnology advances, it is possible to build nanomachines to conduct tasks on the nano-scale. Since the EM wave, the traditional communication medium does not apply in nano-scale, Molecular Communication (MC) has been recently given increasing attention for its excellent biocompatibility and low energy consumption within the human body. Diffusion channel-based MC(DbMC) is mainly studied in the aquatic environment. However, due to the randomness of diffusion, DbMC suffers high losses, low propagation speed, and limited communication range. Directional Molecular Communication(DMC) is proposed by introducing chemotaxis. DMC can significantly improve the efficiency of molecular communication because it keeps molecules moving along a predetermined path. It is particularly suitable in the scenario of target tracking related to some applications such as drug delivery. In this paper, we have proposed a novel massive beacon coordinates system model to aid target tracking. Beacons in this system navigate nanomachines, and the beacon system can uniquely determine their position coordinates. Each nanomachine carries a lot of bacteria carrier (E.coli) to share information. Information is encoded in DNA molecules and transferred to other nanomachines by bacteria carriers. With the help of bacteria carriers, nanomachines can share their current position information with others to realize cooperated fast target tracking. We have evaluated its performance in target tracking through simulation by comparison with the diffusion-based model. Some key factors that may influence target tracking are also taken into consideration.