Soft ferromagnetic properties of nano-crystalline metallic glass considerably depend on microstructure and its magnetic domain structure. Here, we investigated the microstructure evolution and its impact on magnetic domain structure, coercivity (Hc), and saturation flux density (Bs) by manipulating nano-crystallization behavior of Fe–Si–B commercial metallic glass. We revealed that mean grain size of system is affected by both annealing temperature and resulting crystalline phases owing to the competition between grain growth of α-Fe(Si) matrix phase and grain refinement by secondary phase Fe2B formation. As a result, the changed grain sizes played a significant role in deciding the Hc and Bs. However, Hc of nano-crystalline structure increased than that of amorphous state. Our findings will give insight to producing soft ferromagnetic metallic glass by controlling microstructure and domain structure.