A magnetic navigation control apparatus includes a sensing unit, a control unit and a magnetic field generating unit. The sensing unit generates a sensing signal according to the position of a magnetic element. The control unit is electrically connected with the sensing unit and generates a first control signal and a second control signal according to the sensing signal. The magnetic field generating unit is electrically connected with the control unit and has a housing, a plurality of interpoles, and a plurality of short poles. The interpoles are disposed in the housing. The short poles are disposed between the interpoles evenly. The magnetic field generating unit generates a navigation signal according to the first control signal, thereby controlling the magnetic element to move in at least one direction within a target region. The magnetic navigation control apparatus has greater magnetic navigation effects, and can thus reduce the cost.