The present invention provides a system and a method for analyzing jitter of various signals including measurement signals and simulation signals. The method includes the steps of: (a) obtaining a signal file; (b) identifying a type of the signal file; (c) defining a jitter analysis mode from a phase jitter mode, a periodic jitter mode and a cycle jitter mode; (d) obtaining an n-bit differential signal from the signal file; (e) rebuilding an ideal clock based on the differential signal by means of performing a Minimum Deviation Algorithm (MDA); (f) calculating and analyzing jitter of the differential signal according to the ideal clock by means of performing the MDA; and (g) generating and outputting a jitter analysis wave and jitter analysis results according to the defined jitter analysis mode.