A large number of nonlinear, impacting and fluctuating loads are used in power system and make it complex. And unsteady signal will be produced. The traditional measurement method and algorithm of electric power are not accurate for the unsteady signal. This paper firstly adopts a measurement method that calculates the energy of fundamental wave and the distorted part separately. And then proposes an algorithm with fast S transform based on binary sampling. The theoretical analysis shows that the measurement method that calculating the energy of fundamental wave and the distorted part separately is more reasonable. The form of kernel function of fast S transform is fixed not like the lifting wavelet transform whose basis function is hard to choose. And fast S transform will save more time than S transform with similar precision. Finally according to the simulation, it can be concluded that the accuracy of electric energy measurement algorithm with fast S transform based on binary sampling is better than lifting wavelet transform algorithm for both steady signal and unsteady signal. And its efficiency is higher than S transform.