Abstract: Friction stir welding was performed on joining T4003 ferritic stainless steel by using a tungsten rhenium (W-Re) alloy tool. The weld formation, microstructural characteristics, and mechanism of defect formation in the weld were examined. It was showed that the axial pressure of tool monotonously increased with the increasing of welding speed under different rotational speeds. Defect-free welds were successfully produced at rotational speeds of 150 and 250 r/min. However, wormhole defects were produced near the advancing side of the stir zone in the welded joints at the rotational speed of 350 r/min. This phenomenon tended to decrease with the increasing of the tool axial pressure and welding speed. A phase transformation and significantly harden occurred in the stir zone of the welded joint, and the microstructure in this region changed to very fine grains consisting of duplex structure of equiaxed ferrite and low carbon martensite. An uneven hardness distribution in the weld was observed. Moreover, a balanced-flow model of weld metal was proposed, and employed to analyze the mechanism of defect formation in the weld.