The present disclosure provides an overlay metrology method, an overlay control method and an overlay control system. The overlay metrology method includes capturing a current layer image of a current overlay mark on a current layer with a current focal length and capturing a previous layer image of a previous overlay mark on a previous layer with a previous focal length. Then, the overlay metrology method further includes combining the current layer image with the previous layer image to form an overlay mark image and determining an overlay error between the current overlay mark and the previous overlay mark based on the overlay mark image.