The purpose of this work is to analyze the effect of structure parameter disturbance on the dynamic characteristics of a hydropower station powerhouse. A vibration model with a head-cover system is established, and then the general disturbance problem analysis methods are discussed. Two new formulae based on two types of disturbances are developed from existing methods. The correctness and feasibility of these two formulae are validated by analyzing the hydropower station powerhouse vibration model. The appropriate calculation method for disturbance of the hydropower station powerhouse vibration dynamic characteristics is derived.