Abstract: Frequency spectrum analysis has been widely used in the area of signal processing. A method of frequency analysis in time domain is presented in this paper. The relation of frequency spectrum analysis and frequency analysis in time domain is discussed. The method of transient frequency analysis and its applications on underwater acoustic signal processing is introduced. The experimental resultS both in a lake and at the sea meet with that of theoretical analysis and simulation in computer. The estimator of transient frequency variance used to detect short CW pulse has improved the detective ability of a system in the background with pulse interference significantly.