In this study, based on the principles of bionics, we fabricated a bionic non-smooth concave pit structure on the shoulders of friction stir welding tools and detected the thermal cycling curve, downforce, and torque of the tool in the welding process. We tested the wear loss weight and analyzed the surface morphology of the shoulder surfaces after welding for 200 m. This study found that as the distance between the concave pits decreased and the number of concave pits increased, the maximum downforce, torque, and temperature in the welding process showed a decreasing trend. As the speed increased, no matter how the tool structure changed, the downforce and torque decreased, while the peak thermal cycle temperature increased. The experimental welding results show that the wear loss weight of the non-smooth structure tool significantly reduced. The lowest wear loss weight of the tool with a concave pit interval of 1.125 mm was only 0.1529 g, which is 27% lower than that of the conventional tool. Our observations of the surface morphology of the tool shoulder after welding showed that the amount of aluminum swarf on the tool shoulder of the welding tool gradually declined with the increasing density of the uneven pits. The lowest number of aluminum chips adhered to a welding tool with a pit distance of 1.125 mm. Therefore, friction stir welding tools with biomimetic structures have better wear resistance and adhesion resistance.