The invention discloses a male and female graine laser separator and a separation method thereof. The separator comprises an elevated working platform, an egg raising paper positioning system, a graine color image processing system, a laser generation and light deflection scanning and egg launching system, and a computer. The separation method comprises the following steps: starting the separator, resetting the shifted working platform, placing egg raising paper on a negative-pressure adsorption platform, and starting an air pump to absorb the egg raising paper to be flat; starting a color image acquisition program, and controlling a color image sensor to shoot an egg raising paper image and transmit the egg raising paper image to the computer which processes data, gives out a work instruction for launching time-sequence laser pulse to a laser generator and an electric control device, and gives out a work instruction for light deflection scanning to a galvanometric scanning and electric control device, and generating laser beams to shoot female graine; and placing novel egg raising paper after the task is completed, and repeating the steps. The separator can automatically and accurately separate male and female graines with different graine colors at a high speed so as to save labor and improves the separation precision.