The invention discloses a vibration isolator deformation measurement tool and a measurement method thereof. The vibration isolator deformation measurement tool comprises a first transition piece; the first transition piece is fixed on the surface of a device base via a magnetic base; the first transition piece is vertically connected with a second transition piece; a mobile digital display device is arranged on the second transition piece; a third transition piece is connected on the mobile digital display device; and a positioning pin is arranged on the third transition piece in a sliding mode. In the case of measurement, a corresponding combination hole is selected to connect the first transition piece and the second transition piece, the first transition piece is then fixed on the surface of the device base via the magnetic base, and the magnetic base is adjusted to enable the positioning pin to be contacted with the top part and the bottom part of the vibration isolator; and the positioning pin is adjusted and the third transition piece is moved, the positioning pin can be contacted with the top center and the bottom center of the vibration isolator, data are read to obtain a height value after vibration isolator deformation, and the difference with a normal height value of the vibration isolator is the deformation amount before and after mounting of the vibration isolator. The mounting deformation amount of the vibration isolator can be accurately measured, the purpose of controlling the deformation amount of the vibration isolator is achieved, the structure is simple, the operation is easy, universality is good, and the cost is low.