The nugget offset is the main challenge in the resistance spot welding (RSW) of unequal thickness plates. Magnetically assisted resistance spot welding (MA-RSW) is a potential new process to reduce the nugget offset ratio. Aiming at analyzing the fluid flow mode of the MA-RSW with unequal thickness plates, a multi-physics finite element model, including distortion field, thermal field, electric field, magnetic field, and fluid field, was created. The experimental validation verified the accuracy of the model. The connection between magnetic fields and nugget shape was analyzed. The results show that the fluid flow modes in the MA-RSW are composed of two parts, namely, the circumferential flow in the horizontal section and the approximately mirror-symmetrical flow in the vertical section. The circumferential motion is intensified with increasing magnetic flux density, and thus, the liquid metals with higher magnetic flux density tend to expand toward the solid–liquid interface, leading to nugget growth in these areas. Finally, based on the numerical results, a process of minimizing the nugget offset is proposed. The experimental results indicate that the proposed process can improve the nugget offset in RSW of unequal thickness plates.