Sea skimming and high-maneuverability anti-ship cruise missiles have been designed to evade the surveillance and tracking of maritime multi-functional radar (MFR), resulting in difficulties in radar target tracking. Sea skimming and high maneuvering cause two problems: distortion of the estimated elevation angles by multi-path echoes and overload of radar beam resources by precise tracking tasks. Recently, a dual-band MFR has been developed for state-of-the-art battleships. In this study, a dual-band MFR system is used to improve the tracking accuracy of sea skimming and high-maneuvering targets. In particular, the fusion and allocation of dual-band MFR echoes to address the problems caused by multi-path echoes and heavy precision tracking tasks can lead to improved tracking accuracy. The simulation results revealed that our proposed method is capable of performing successful tracking of sea skimming and high-maneuvering targets in a dual-band MFR system.