Friction stir welding was conducted on AZ31B magnesium alloy. Variation of microstructures and properties of the welding joints before and after heat treatments was studied. The results show that post-weld heat treatments can markedly improve the mechanical properties of the friction stir-welded AZ31B magnesium alloy joints; when the rotating speed of stirring pin is 600 r·min-1 and the welding speed is 47.5 mm·min-1, the ultimate tensile strength can reach 168 MPa and the elongation is 3.6%. After heat treatments, the highest ultimate tensile strength can reach 205 MPa, which is 22.02% higher than that before heat treatments and the elongation is 8.6%, which is 138.89% higher than before heat treatments. The ideal heat treatment technique of the joint is keeping the annealing temperature at 250 oC for 1 h. As the annealing temperature increases, the growing speed of welding nugget zone grain is higher than the heat affected zone/thermo-mechanically affected zone. When the annealing temperature is higher than 250 oC, the morphologies of tensile fracture of welding joints mainly exhibit oblate dimples with a typical ductile dimple-fracture.