Two analytical models of a typical two-stage vibration isolation system are established from the point of view of vibration power transmission and engineering practices. Considering the distributed parameter characteristics of the elastic raft, isolators and flexible foundation, dynamic equations of each subsystem are derived using the mobility matrix approach. The mechanism of the vibration transmission is revealed using the concept of power flow. Meanwhile, general rules which should be followed when designing the two-stage isolation systems are discussed. It is shown that the moment excitations play an important role in the vibration transmission process. Hence, the injection of power caused by the moment excitations should be reduced. In the permitting condition of the energy efficiency and installation spaces, a better isolation effect will be obtained when appropriately enlarging the intermediate mass. The distribution parameter characteristics of the elastic raft, isolators, and non-rigid foundation can lead to a deterioration of performance in the high-frequency domain. Using the scheme of the dispersion intermediate mass can effectively avoid the impact of the flexible raft, and can also significantly inhibit the interaction between the wave effects caused by the isolators and modals of the flexible raft, which may input more power to the installed foundation.