The invention discloses a method for controlling movement of heads of flat knitting machines.The method includes acquiring first target values for defining first stroke of the heads; correcting the first target values according to the positions of effective units in the heads so as to obtain second target values for defining second stroke of the heads; allowing the heads to move under the control according to the second target values.The second stroke is shorter than the first stroke.The invention further correspondingly discloses a system for controlling movement of the heads of the flat knitting machines.Owing to the mode, the method and the system have the advantages that the heads can be prevented from moving by redundant stroke, and accordingly the knitting efficiency of the flat knitting machines can be improved.