From acoustic point of view, the characteristics of the submarine are numerous vibration and noise sources, the serious coupling among them and the complex transmission path. Hierarchy diagnosis resolves the problem of the vibration and noise source separation and quantification by constructing hierarchical structure, and the dominance relationship is formed from top to bottom. By means of scale, the vibration and noise source’s contribution is obtained by pairwise comparison. According to the decibel addition principle, the AHP comparison scale is adjusted for physical significance, and the result of the hierarchy diagnosis is the measure with actual physical significance. The hierarchy diagnosis procedure of the submarine is divided into two links: they are from the equipment to the shell and the shell to the underwater acoustic field. The results are fused by weighted averages method and D-S evidence theory. The feasibility of this method is validated by simulation and cabin test.