The stern rudder of an underwater vehicle has a significant impact on the wake field and the flow noise. Hence, it is important to optimize the design of the stern rudder for reducing the radiated noise. In this work, a numerical model is set up to predict the flow noise of the underwater vehicle, based on the LES turbulence model and FW-H acoustic analogy method. After the verification study, the numerical prediction of the flow noise is compared with the experimental measurements to verify the accuracy of the numerical model. Then, the influence of sails on the flow noise is explored. It is observed that the existence of the sail significantly increases the noise at the low frequency. Furthermore, to examine the influence of the stern rudder type, the sound pressure levels of underwater vehicles with three full appendages having cross-type rudders, X-type rudders, and T-type rudders, are compared. The strong interaction between the sail’s wake and the stern rudder is evident. The underwater vehicle with T-type rudders exhibits the lowest sound pressure. In addition, the influence of the stern rudder type on the directivity of sound pressure levels is also presented.