In the recent progress in terahertz (THz) devices, various kinds of source devices, such as resonant tunneling diodes, quantum cascade lasers and so forth, have been developed. Frequency measurement of THz radiations, which can operate in high speed and at room-temperature, is important for development of high-performance THz source devices. Recently, frequency measurement using optical combs are demonstrated by several groups. In these techniques, modelocked lasers (MLLs) are used for optical comb source, so that phase-locking techniques are required in order to stabilize the repetition frequency of the MLLs. On the other hand, a modulator-based optical comb generator has high accuracy and stability in the comb spacing, which is comparable to that of microwave signal driving the modulator. Thus it is suitable for frequency measurement of THz waves. In this paper, we demonstrated frequency measurement of THz waves using a Mach-Zehnder-modulator-based flat comb generator (MZ-FCG). The frequency measurement was carried out by an electro-optic (EO) sampling method, where an optical two-tone signal extracted from the optical comb generated by the MZ-FCG was used for the probe light. A 100 GHz signal generated by a W-band frequency multiplier and the probe beam collinearly traveled through an EO crystal, and beat signals between them were measured by a combination of a balanced photodetector and a spectrum analyzer. As a result, frequency measurement of the 100 GHz wave was successfully demonstrated, in which the linewidth of the beat signal was less than 1 Hz.