Herein, the effect of the ordered phases and microstructure of 6.5 wt% Si electrical steel recrystallized and quenched at different cooling rates on its iron loss is investigated. The varied cooling rate barely influences the grain size and the precipitation of Cu but affects the magnetic domain significantly. A higher cooling rate is associated with greater residual stress and hence, leads to an increase in the width of the magnetic domain. In terms of the ordered phases, the quantity of B2 first decreases and then increases with a rising cooling rate while the quantity of D03 decreases. Meanwhile, the size of B2 antiphase domains reduces, while the D03 antiphase domains are either too fine to be observed or absent at higher cooling rates. The increased residual stress, the refinement of B2 antiphase domains, and the associated larger pinning effect on the migration of magnetic domain walls jointly lead to higher hysteresis loss. In addition, the increased width of the magnetic domain results in a larger anomalous loss. Both effects give rise to an overall increase in the iron loss P10/50.