Real-time DOA (direction of arrival) estimation of surface or underwater targets is of great significance to the research of marine environment and national security protection. When conducting real-time DOA estimation of underwater targets, it can be difficult to extract the prior characteristics of noise due to the complexity and variability of the marine environment. Therefore, the accuracy of target orientation in the absence of a known noise is significantly reduced, thereby presenting an additional challenge for the DOA estimation of the marine targets in real-time. Aiming at the problem of real-time DOA estimation of acoustic targets in complex environments, this paper applies the MEMS vector hydrophone with a small size and high sensitivity to sense the conditions of the ocean environment and change the structural parameters in the adaptive adjustments system itself to obtain the desired target signal, proposes a signal processing method when the prior characteristics of noise are unknown. Theoretical analysis and experimental verification show that the method can achieve accurate real-time DOA estimation of the target, achieve an error within 3.1° under the SNR (signal-to-noise ratio) of the X channel of −17 dB, and maintain a stable value when the SNR continues to decrease. The results show that this method has a very broad application prospect in the field of ocean monitoring.