This paper introduces a SER (soft error rate) analysis algorithm using a frequency method which provides a fast and accurate technique to calculate the effects of electrical masking and latching window masking. The frequency method is an approach to analyze the propagation of transient fault using frequency features of each logical gate and signal. It is divided into two procedures, one is linear system procedure, the other is nonlinear system procedure. In linear system procedure, the frequency method calculates the output signal by the frequency response of electrical system. In nonlinear system, the transient faults magnitude is high enough, and transistor passes through different linear systems and causes the top of signal smoothed over. We calculate the output signal of the nonlinear system using input-output feature of electrical system. The functional relationship of the pulse-width of the output signal and the pulse-width of the particle-strike-caused glitch can be calculated by a data fitting method. In this paper, the frequency method and data fitting method are applied to model the probabilities of errors caused by a the particle strike. The experimental results with inverter chains show that the proposed technique achieves 96.96% accuracy and has proved to be time efficient compared with HSPICE simulation. At the same time, the experiments with ISCAS85 benchmark circuits and multiplier array also achieve 95.82% accuracy.