Thermal cycles and deformations during high-speed micro friction stir welding (μFSW) under different welding conditions were studied by experimental methods. The results show that the peak temperature and elevated-temperature exposure time (t150) increased with the increasing of rotational speed and decreased with the increasing of welding speed. Increasing rotational speed or welding speed led to an increase in both heating and cooling rates. The joint fabricated by the pinless tool experienced a lower peak temperature, a shorter elevated-temperature exposure time, and a larger temperature gradient than that by the pin tool. The welded sheet presented an anti-saddle deformation character, with convex bending in a longitudinal direction and concave angular bending in a transverse direction. In comparison to the pin tool, the longitudinal maximum bending deformation, Zmax, of the joint fabricated by the pinless tool was reduced by 12.35%, and the transverse angular deformation, α, was reduced by 6.67%. In comparison to the steel backing plate, the Zmax of the joint produced using a copper backing plate was reduced by 40.66%, but the α was increased by 53.27%.