Generally, AZ31 magnesium alloys have poor formation ability near room temperature. This material, with ultrafine grains, usually exhibits excellent superplasticity at high temperature. Therefore, the preparation of materials with suitable microstructures to obtain the superplasticity is an important goal. In this study, the double-side FSW (Friction Stir Processing) process was applied on the AZ31Mg alloy to obtain the microstructure with ultra-fine grains. The effect of the FSW on the microstructure and the mechanism of microstructure evolution was elaborated. Meanwhile, the effects of deformation parameters, temperature, and strain rate on flow behavior and superplasticity of the joint were systematically and comparatively studied. It was found that the microstructure at the joint center with double-side FSW could obtain much finer grains with an average grain size of 9.6 μm compared with the rolled materials (25.9 μm). The high temperature deformation results showed that the optimum elongation (446%) was achieved with the deformation temperature of 450 °C and strain rate of 0.0003 s−1, which was far greater than the elongation of the room temperature (20.8%). The mechanism of parameters on deformation behavior of the joint samples was elaborated.