Low temperature friction stir welding (including below A1 point) was successful for three types of carbon steels with different carbon contents (IF steel, S12C, S35C). For all the carbon steels, the strength of the FSW joints increased when compared to that of the normal structure (ferrite + pearlite) of base metal. Compared with IF steel, the microstructures and mechanical properties of the carbon steel joints are significantly affected by the welding conditions due to the phase transformations. For the S12C steel, the welding produces a ferrite-pearlite structure, and the strength slightly increases with the increasing welding speed (decreasing the heat input) due to the refined microstructure. For the S35C steel, under the conditions exceeding the lower critical cooling rate, martensite was formed, resulting in a significantly increased joint strength; while under the conditions when martensite is not formed, the strength of the joint increased with the increasing welding speed (decreasing the heat input) due to the refined microstructures. Thus, friction stir welding enables us to control both the maximum temperature and the cooling rate in order to produce higher strength joints.