A method and system of controlling a multi-leaf collimator, wherein steps of the method includes: receiving treatment data, and the treatment data includes position information of N treatment points, conformal position information of N treatment points and radiation field shapes of N treatment points; controlling a treatment head to a conformal position of a first treatment point, and controlling the multi-leaf collimator to begin to conform to a radiation field shape of the first treatment point so as to start a treatment of the first treatment point; controlling the treatment head to a conformal position of a Kth treatment point, and controlling the multi-leaf collimator to begin to conform to a radiation field shape of the Kth treatment point so as to start a treatment of the Kth treatment point; carrying out the described operations repeatedly until the conformation of the radiation field shape and the treatment of all treatment points are completed.