During the thin slab continuous casting process of silicon steel, electromagnetic stirring (EMS) can control the flow, heat transfer, and solidification of molten steel through electromagnetic force. Herein, a 3D mathematical model coupling the fluid flow, heat transfer, solidification, and the electromagnetic field is built. The effects of varied current intensities on the flow, heat transfer, and solidification of molten steel in the thin slab under secondary EMS are explored based on applying the electromagnetic brake in the mold region. In the findings, it is demonstrated that increasing the current intensity increases the flow rate and vorticity of the molten steel in the second cooling zone, eliminating the superheating phenomenon and improving the uniformity of the molten steel's temperature distribution. Meanwhile, based on the nucleation and growth parameters determined from thermal simulation experiments, the cellular automation finite‐element model is used to simulate the microstructure evolution during the solidification of thin slab. In the results, it is shown that the stirring energy increases when the current intensity increases, potentially promoting equiaxed crystal growth and grain refinement. Compared to the production sample, a reasonable qualitative agreement is achieved for the grain morphology, equiaxed crystal ratio, and columnar to equiaxed transition.