In the marine gear system, the vibration of gears is transmitted to the ship foundation through shafts, bearings, housing, and isolators, and then the underwater noise is generated. Analyzing the vibration transfer properties and identifying the critical path can provide guidance to the low-noise design of the gear system. In this paper, a coupled gear-housing-foundation dynamic model is proposed for a flexible supported gear system, in which the flexibility of each subsystem and the coupling relationship between them are taken into account. The transferring process of gear vibration is divided into different layers between gears, shafts, bearings, housing, isolators, and ship foundation. Based on the vibration power flow (VPF) theory, detailed layering vibration transfer path analyses of the gear isolation coupled system are carried out for both location path and direction path, and the main paths are identified in a broad speed range. The results indicate that though the gear vibration transferred to the foundation attenuate layer by layer, there may be reverse VPF in some special location path and direction path under resonance conditions.