The invention provides an automatic course control system of a rudderless ship. The automatic course control system comprises a GPS compass, a ship control apparatus, a propeller propulsion device and a rotation speed sensor. The ship control apparatus comprises a man-machine operation interface. The propeller propulsion device comprises a left propeller and a right propeller which are symmetrically installed at the stern, an engine and an engine controller. A current navigation speed and a current navigation angle measured by the GPS compass are computed with a target navigation speed and a target navigation angle which are input into the man-machine operation interface respectively and thus a target control rotation speed is obtained. The ship control apparatus carries out operation on an actual rotation speed of the propeller measured by the rotation speed sensor and the target control rotation speed, and the engine controller controls the engine to adjust the rotation speed square difference of the propeller. The invention further relates to an automatic course control method of the rudderless ship. The beneficial effects of the automatic course control system and method of the rudderless ship are that the system is simple in structure, technical requirement is low, cost is low, and the system and the method are easy to popularize and apply.