This study focused on the six-phase transverse magnetic field flux switching linear magnetic suspension motor (SPTMFFSLMSM) used in rail transit. The armature windings, excitation windings, and permanent magnets are all located on the mover iron core, enabling the motor to achieve traction, levitation, and guidance simultaneously. Due to the unique structure of the SPTMFFSLMSM, heat dissipation is challenging, which can lead to significant temperature rise and negatively affect the motor′s operating characteristics. To address the issue of severe temperature rise in the mover iron core, a cooling system was designed to ensure normal motor operation. First, a three-dimensional steady-state temperature field mathematical model was established based on the motor′s structure, and the boundary conditions were derived. Then, the thermal parameters of various materials inside the motor were determined, and the motor′s heat sources and losses were analyzed, with the corresponding heat generation rates calculated. Finally, the motor′s temperature field was analyzed using a three-dimensional finite element method under both natural cooling and forced water cooling conditions, and the temperature distributions of the two cooling methods were compared. The results showed that the water cooling system effectively reduced the temperature of the mover iron core, verifying the effectiveness and feasibility of the designed cooling system.