In turbine tenon joint structures, fretting fatigue is common and can have detrimental effects on the components. To increase the fretting fatigue life, the design of tenon joint structures must be optimized. A parametric model of the three-tooth mortise and tenon joint structure is developed in this research. Sensitivity analysis yields the primary characteristic parameters, which are then employed as design variables. The objective function is the life of fretting fatigue. An aero-engine turbine three-tooth mortise and tenon joint structure was optimized against fretting fatigue using a Multi-Island Genetic Algorithm (MIGA), which was then experimentally verified. The optimization was based on the multidisciplinary optimization platform ISIGHT to write batch files integrating ANSYS and MATLAB. According to the findings, the three-tooth mortise and tenon joint structure’s fretting fatigue life can be increased by 51.3% by applying the MIGA. The contact pressure was reduced by 0.54% and the maximum slip amplitude has been reduced by 13%. The approach of optimization’s efficacy was confirmed.