A frequency measurement method and a system thereof are provided. The method includes: generating to-be-detected emergent light under an action of the electro-optical crystal when a light source irradiates an electro-optical crystal disposed in the microwave electric field; detecting, by a single-photon detector, the to-be-detected emergent light to obtain a detection result of the single-photon detector; and determining a frequency of the microwave signal based on the detection result of the single-photon detector and a Fourier transform algorithm.