Fixed time sampling is commonly used in the hydropower on-line monitoring system， which requires tremendous data collection. The inconsistent frequency of sampling and signal in frequency spectrum analysis may cause leakage of frequency and phase excursion， affecting the correct representation of the state of the system. By applying synchronous whole-periodic sampling， that is， each starting point of data collection is determined according to the key signal， which provides the same phase datum for every data collection. Every time the rotor makes a circle， a fixed amount of data is collected， so that both the leakage effect and picket fence effect in frequency spectrum analysis are prevented. And the phase in the signal can be exactly extracted， improving the accuracy of data collection and analysis.