The invention relates to a preparing method of a circuit board with a misalignment structure, which comprises the following steps: arranging a sticking area on the conductive circuit layer of a first base plate before pressing the first base plate and a second base plate, arranging a first removing area, a second removing area and a third removing area matched with the sticking area in shape and size in the middle of the surface of the conductive layer of the second base plate, arranging a first cutting slot and a second cutting slot which pass through the second base plate and are respectively connected with the first removing area and the second removing area on both ends of the third removing area, sticking the conductive circuit layer to the surface of the conductive layer, pressing the first base plate and the second plate by the mode that the sticking area corresponds to the third removing area and a notch, using rubber material for filling the notch, and cutting along the edgesof the first removing area and the second removing area to remove the first base plate and the second base plate which correspond to the first removing area and the second removing area and the second base plate which corresponds to the third removing area. The preparing method can prevent the conductive circuit which corresponds to the second base plate from being damaged when the second base plate which corresponds to the sticking area is removed.