Impulsive near field earthquakes often exhibit different characteristics from far field earthquakes due to the larger velocity pulses they produce. In order to study the effects of near fault ground motions and foundation stiffness on the structural dynamic response of the pressure regulating towers, taking a proposed pressure regulating tower project as the research object, we established a three dimensional finite element model of water-structure-foundation using ABAQUS with the consideration of fluid-solid coupling and foundation radiation damping. Three different types of seismic records from the 1999 Chi-Chi earthquake, namely, far field, non impulsive near field and impulsive near field earthquakes, were introduced to the model for the dynamic analysis of the structure using a fluctuating input method with high accuracy and a viscoelastic artificial boundary. The study shows that the input ground motion characteristics and soil-structure interaction have significant effects on the structural response of the pressure regulating tower, and the displacement response of the impulsive near field earthquakes is more than 2.5 times larger than that of the far field earthquakes when the foundation stiffness is small, and the whiplash effect is more obvious. The effects of impulsive near field earthquakes on the structure is highly correlated with the first period of the structure. The results of the study can provide a theoretical basis for the design of high hydraulic structures in the near field region.