As the basic carrier of long-distance inter-basin water conveyance project of pressure piping, pressure piping is an important part of agricultural engineering and water conservancy projects, which plays an important role in solving the uneven spacetime distribution of water resources. The vibration during the operation is the critical problem in the design and safety evaluation of water pipeline. In order to solve the problem of how to improve the precision of the FSI (fluid-solid interaction) model in the natural vibration characteristics analysis of the piping, two different FSI models of a piping in cascade pumping station of Jingdian Project were built, by using the additional mass method and direct coupling method respectively. Then the modal characteristics of two FSI models which were obtained in the natural vibration characteristics analysis were compared with the modal characteristics of the prototype piping identified by stochastic subspace identification (SSI) method. The comparison results show that the simulation results of the model by using direct coupling method were in good agreement with the results identified by SSI method, and the maximum error was 3.62%. In the comparison of calculation accuracy of the same order, the model by using direct coupling method outperforms the model by using additional mass method, making up for the lack of the modes that the additional mass model can not work out. The results show that FSI affects the piping system modal frequency seriously and the model by using direct coupling method is superior to the additional mass model in terms of the order number and precision of the simulation, reflecting the real natural vibration characteristics of liquid conveying piping. This method can be used in the analysis of the dynamic characteristics of complicated pipe systems.