In this paper, the vibration frequency of the stator of 3.6 MW fully immersed evaporative cooling permanent magnet semi-direct drive generators (ECPMSDDGs) was analyzed based on the fluid-structure coupling theory and solved by finite element analysis (FEA) simulation. The resonance noise reduction research under the typical working condition induced by two-phase flow and electromagnetic force was studied based on the method of structural optimization. In this paper, a structural optimal design method for the stator of the 3.6 MW ECPMSDDGs was presented. First of all, the frequency and characteristics of electromagnetic force of 3.6 MW ECPMSDDGs under the rated power were analyzed. Secondly, the frequency and characteristics of two-phase flow boiling vibration were analyzed based on the bubble oscillation theory of the two-phase flow and the experiment. Thirdly, the wet modal natural frequency of the stator core cooling structure was analyzed based on the fluid-structure coupling theory and FEA. Finally, the natural wet mode vibration frequency of the stator cooling structure of the 3.6 MW ECPMSDDGs was improved based on the structure optimization. This optimization method could reduce the resonance noise of evaporative cooling motor induced by electromagnetic and two-phase flow. The optimization results showed that the natural wet mode frequency of the stator could be improved by optimizing the radial flow groove and supporting beam under the condition that the effective length of the stator core remained unchanged during the optimization. The noise simulation result showed that the resonance noise of 3.6 MW ECPMSDDGs induced by electromagnetic and two-phase flow could be reduced after the structural optimization.