The invention relates to the field of medical endoscopic applications, in particular an electronic endoscopic navigation system, comprising an operation desk, an annular scanner and a magnet which is fixed in an electronic endoscope, the operation desk penetrates the center of the annular scanner and is parallel to the axial direction of the annular scanner, a plurality of electromagnets are radially distributed in the annular scanner, and controlled by a control device. The electronic endoscopic navigation system generates a magnetic field by the electromagnets in the annular scanner, thus being taken as the power for the movement of the pellet endoscope; the movement of the pellet endoscope is controlled by an operator by changing the strength and the direction of the magnetic field, and then image information is conducted by the pellet endoscope, thus achieving the operations of observation, taking pictures, photography and so on of bladder, stomach and other parts of human body. The electronic endoscopic navigation system can freely move and change the direction of a lens without other contact operations and controls, thus having favorable adaptability and maneuverability.