Friction stir welding (FSW) has been validated to be a severe plastic deformation method for development of ultrafine-grained metals. In this study, hot-rolled AZ31 magnesium alloy plate was processed by FSW, and the effect of FSW on the low-cycle fatigue (LCF) behavior of AZ31 magnesium alloy was analyzed. Results showed that the interface between the stir zone and thermo-mechanically affected zone at the advancing side is the weakest region, in which the monotonic tensile and fatigue fracture occur. Compared with the base metal (BM), the LCF fatigue life, the yield strength, the ultimate tensile strength and the elongation of FSW specimen decrease. The main deformation during LCF was dislocation slip deformation. The fracture surface exhibited a typical fatigue characteristic with the fatigue striations. Finally, we found that the LCF behavior of BM and FSW specimens can be well described by the Coffin-Manson and Basquin’s relations.