The invention discloses a multi-leaf collimator control system, a method thereof and a device and a storage medium, and the system comprises a measurement module which is used for triggering a light beam shielding signal of an optocoupler switch, and the measurement module comprises at least one measurement assembly with a through hole; the optocoupler switch comprises a light beam generator and alight beam receiver, and the light beam receiver is used for receiving the generated light beam shielding signal; an encoder is used for generating and recording position information of the measurement module; a driver is used for driving the measurement module to move; and a controller is in communication connection with the optocoupler switch, the encoder and the driver, is used for controllingthe driver to drive the measurement module to move according to a preset moving rule, and is correspondingly used for acquiring the position information of the measuring module generated by the encoder and carrying out zero calibration on the leaf based on the position information. According to the embodiment of the invention, the position information of the leaf assembly is obtained through a preset movement rule, so that the zero-calibration position of the leaf assembly is more accurate.