The invention discloses a measuring system of relative position of a laser mode and an aperture and a measuring method thereof, and mainly solves the disadvantage of low measurement precision of present systems. The whole system comprises a laser (1), an optical system (15), a resonator to be measured (6), a spectroscope (7), a total reflective mirror (8), an image acquisition and data acquisition system (16), a main control computer (13), and a piezoelectric ceramics driver (14); the piezoelectric ceramics driver drives the laser to output laser; the optical system is adjusted to allow the laser outputted by the laser to be coupled to the resonator to be measured; the laser outputted by the resonator to be measured are divided into two paths by the spectroscope and the total reflective mirror; the two-path laser is collected and transmitted to the main control computer by the image acquisition and data acquisition system; the main control computer processes images of the aperture andthe laser mode by using a high-precision image processing algorithm, and calculates the central coordinates of the aperture and the laser mode respectively. The invention has the advantages of synchronous CCD camera acquisition and sawtooth wave signals, and high measurement precision, and is applicable to the high-precision automatic regulation of the laser.