In a departure from the past, unmanned underwater vehicles (UUVs) and unmanned surface vehicles (USVs) are increasingly needed for complementary cooperation in military, scientific, and commercial applications, because this is more efficient than standalone operations. Information sharing through acoustic underwater communication is vital for complementary cooperation between USVs and UUVs. Normally, since USVs have advantages in terms of wide operational boundaries compared to UUVs, they are efficient for tracking UUVs. In this paper, we suggest a UUV tracking algorithm for a USV. The tracking algorithm’s development consists of three main software models: an estimation based on an extended Kalman filter (EKF) with a navigation smoothing method, guidance based on multimode guidance, and re-searching based on a pattern. In addition, the algorithm provides a procedure for tracking UUVs in complex acoustic underwater communication environments. The tracking algorithm was tested in a simulated environment to check the performance of each method, and implemented with a USV system to verify its validity and stability in sea trials. The UUV tracking algorithm of the USV shows stable and efficient performance.