Good high-frequency magnetic softness and thermal stability are very important for the wide application of Fe-based nanocrystalline alloys. The present work reports the influence of Mn-doping and rapid annealing on the magnetic softness, nano-structure, and magnetic-microstructure of Fe76−xSi13B8Nb2Cu1Mnx (x = 0, 1, 2, 3, and 4) alloys. It was found that the Fe74Si13B8Nb2Cu1Mn2 alloy exhibits a superior magnetic softness with the high-saturation magnetic induction of 1.32 T and a large permeability at 100 kHz of over 15,000 at a large annealing-temperature region of 120 °C. The microstructure and magnetic domains characterization indicate that the good magnetic softness and thermal stabilization can be ascribed to the superb nano-structural stability caused by the Mn doping and rapid annealing at elongated temperatures, which can maintain a fine and high number density α-Fe(Si) nano-grains and facilitate the formation of regular and wide domains.