The invention provides a novel scanning tunneling microscope design structure using a motor-scanning head separation technique. A motor and a scanning head are separated, the scanning head is clamped at a guide rail independently by a spring piece, and the motor is responsible for pushing the scanning head to a tunnel current zone; and then the scanning head retreats autonomously. The scanning head is composed of a probe, a probe rack, a scanning tube, a corundum pedestal, and a corundum pipe and the like. Therefore, influences on imaging of the scanning head by interference factors like thermal drift and electric fluctuating caused by the motor can be prevented and thus imaging becomes clear.