To solve the obvious errors of the frequency-domain integration when dealing with the measured acceleration data, a modified algorithm is provided to use the EMD′s adaptive features for the frequency domain integration of t he measured acceleration signal, according to the traits of vibration signals of the hydro-generating unit. In the method, the frequency domain integral of the vibration signal is used to calculate the time history data about velocity and displacement. The time history data are divided into many intrinsic mode functi ons (IMFs) by the EMD′s adaptive features, and then these IMFs are filtered according to the environmental noise and the characteristic frequency of the signal of hydro-generating unit. The simulation results show that the relative error is minimal and the correlation coefficient is maximal. The result of processing vibration signals of Jinghong Hydropower shows that integration results accord with the facts. The above analyses conclude that the method is feasibl e for dealing with acceleration signal and is reliable for hydropower vibration signal post-treatment.