The method of operational transfer path analysis(OPA) in engineering application is very attractive. In practical conditions of the ship, the coupled signals which cannot reflect the true vibration characteristics of the equipment can only be measured by the sensors. To deal with this problem, the signals of multi-vibration source were regarded as convolution aliasing. A separation method of coupled vibration source was proposed, then a OPA model of the ship was established. Combined with the test of vibration and acoustic radiation of the ship, the feasibility and correctness of the new model were validated. Two key factors including the number of observation points and the different combination of operating conditions which affected the accuracy of the OPA were were discussed, and the effective selection principles are given. The results indicate that the OPA method can effectively identify noise source of the ship, which is of great significance in guiding a real-time prediction of radiation noise and adopting appropriate measure to reduce structural vibration and radiated noise. Therefore the OPA method established in this paper has broad prospect of engineering application.