The present invention provides a positioning method for shaping large-size stiffened panel made of composite material and a clamping apparatus thereof, which can meet the strict requirements on the position of the stringer and the internal quality of large-size stiffened panel. The method comprises the following steps of: curing the stringer; utilizing a positioning tool to position the stringer on the skin which can be either cured already or not cured yet; and cementing or cementing and co-curing the stiffened panel.