The presently disclosed technology includes a friction stir welding apparatus comprising a frame, a moving platform and a parallel mechanism composed of three branch mechanisms, wherein a first branch mechanism comprises a first sliding pair, a first revolute pair, a telescopic rod and a first spherical pair connected in sequence. A second branch mechanism and a third branch mechanism both comprise a third sliding pair, a second revolute pair, a third linkage and a second spherical pair connected in sequence. The friction stir welding apparatus has high stiffness, low inertia, high dynamic performance and high accuracy, which can achieve precision welding with high requirements on processing quality and accuracy for jointing annular seams of large-scale rocket fuel storage tank barrels in the aviation field, for example. The presently disclosed technology also includes a corresponding friction stir welding system.