Mold electromagnetic stirring (M-EMS) has been introduced into the continuous casting of steel billets to promote the formation of a central equiaxed zone; however, the formation mechanism of the equiaxed crystals and the effect of M-EMS on crystal transport are not fully understood. Currently, a three-phase volume average model was used to study the solidification in a billet continuous casting (195 mm × 195 mm). The modeling results showed that the main function of M-EMS in this type of billet casting is to promote superheat dissipation in the mold region, leaving the liquid core out of the mold region undercooled. Although both, heterogeneous nucleation and crystal fragmentation, are considered to be the origins of equiaxed crystals, M-EMS appeared to impact crystal fragmentation more effectively. A small portion of equiaxed crystals could be brought by the M-EMS induced swirling flow into the superheated zone (upper mold region) and remelted; most equiaxed crystals settled in the lower undercooled zone, where they continued to grow and form a central equiaxed zone. These simultaneous phenomena represent an important species/energy transport mechanism, influencing the as-cast structure and macrosegregation. Negative segregation occurred in the central equiaxed zone, positive segregation occurred at the border of the columnar zone, and a trail of negative segregation occurred in the subsurface region of the billet. Finally, parameter studies were performed, and it was found that the shielding effect of the copper mold, electrical isolation at the strand-mold interface, and relatively high electrical conductivity of the strand shell affect the M-EMS efficiency.