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Simulation accuracy has great effects on power system analysis and control. In this paper, in order to analyze the power system real-time digital simulation error, prony algorithm is used to extract the features of signal. Based on the analysis results of this algorithm, residual similar index was used to characterize the global error of simulation, and then frequency, damping and amplitude similar indexes were employed to represent features error of transient signals respectively. A calculation program for power system real-time digital simulation accuracy evaluation was employed to analyze the measured waveforms and results of fault simulations on RTDS. Simulation results have proved the validity of the proposed analysis method of power system real time digital simulation error.