In view of the limited number of measurement points applied to the data test, it cannot completely reflect the vibration status quo of the hydropower plant structure. Applying the small amount of vibration test data under limited measurement points of hydropower plant, the paper proposed a method which was based on the theory of counter-analysis of the flow-induced vibration of hydraulic structures, and used genetic algorithm to study the inversion problem of the vibration load of underground plant structures in the unit operation process. The practical engineering application shows that this method can make good use of a small number of measured data from the limited measurement points to feedback the vibration displacement changes of the underground plant structures.