This study investigates refill friction stir spot welding (RFSSW) of 2 mm thick ZK61M-T5 magnesium alloy. Sound joints were obtained at rotational speeds of 1000 rpm and 1500 rpm with welding speeds of 30–50 mm/min. At 1000 rpm, micro-pores appeared at the sleeve-affected zone bottom, exhibiting a full-fillet fracture and a maximum ultimate lap shear force (ULSF) of 8.3 kN. Increasing the speed to 1500 rpm eliminated the pores and changed the fracture mode to partial fillet, but reduced the ULSF to 7.7 kN. Higher welding speeds caused the Hook feature to shift from upward to downward. Compared with the base material, grains in the thermomechanically and sleeve-affected zones were refined, while those in the pin-affected zone coarsened with increasing rotational speed. Overall, higher rotational speed increased heat input and mitigated internal defects, but enhanced annealing and Zr segregation, leading to reduced mechanical performance.