The traditional target tracking is a process of estimating the state of a moving target using measurement information obtained by sensors. However, underwater passive acoustic target tracking will confront further challenges, among which the system incomplete observability and time delay caused by the signal propagation create a great impact on tracking performance. Passive acoustic sensors cannot accurately obtain the target range information. The introduction of Doppler frequency measurement can improve the system observability performance; signal time delay cannot be ignored in underwater environments. It varies with time, which has a continuous negative impact on the tracking accuracy. In this paper, the Gauss-Helmert model is introduced to solve this problem by expanding the unknown signal emission time as an unknown variable to the state. This model allows the existence of the previous state and current state at the same time, while handling the implicit equations. To improve the algorithm accuracy, this paper further takes advantage of the estimated state and covariance for the second stage iteration and propose the Gauss-Helmert iterated Unscented Kalman filter under a three-dimensional environment. The simulation shows that the proposed method in this paper shows superior estimation accuracy and more stable performance compared with other filtering algorithms in underwater environments.