Submerged entry nozzle (SEN) clogging is a troublesome phenomenon in the continuous casting process that can induce the asymmetric mold flow, and thus, lowering the steel product quality. In this paper, a mathematical model coupling the electromagnetic and flow fields, was developed to investigate the influence of the SEN clogging rate on the flow field and the influence of electromagnetic stirring (EMS) on the asymmetric mold flow. Slag entrapment index Rc was introduced to quantify the possibility of slag entrapment, and symmetric index S was introduced to quantify the symmetry of the flow field. The results show that as the SEN clogging rate increased, the slag entrapment index Rc increased, while the symmetric index S decreased. EMS can greatly improve the symmetry of the flow field with SEN clogging, but it cannot remove the asymmetric phenomenon completely because the stirring intensity should be controlled below the safe level to avoid slag entrapment.