A locking apparatus for a flap door of a vehicle includes: a body bracket fixed on a vehicle body; a flap bracket fixed on the flap door; a lower side link with a first end connected to the flap bracket and a second end connected to the body bracket; an upper side link with a first end connected to the flap bracket and a second end connected to the body bracket at an upper side of the lower side link; a stopper groove and a stopper protrusion provided on the first end of the upper side link; a locking cam mounted to a rotational shaft of the lower side link relative to the flap bracket, while being in contact with the stopper groove and the stopper protrusion; and a spring installed between the flap bracket and the locking cam to elastically switch a direction of rotating the locking cam.