There has been a relentless pursuit for high thrust-to-weight ratio development in the aeroengine field. To tackle this, the study successfully achieved high-quality joining of GH4065A/IN718 dissimilar superalloys via inertia friction welding that demonstrated excellent interfacial bonding and no significant welding defects. A systematic investigation was performed on the influence of post-weld heat treatment on the microstructural evolution at the joint interface. The results indicated that post-weld heat treatment increased the width of the weld nugget and thermomechanically affected zones via dynamic recrystallization and grain boundary migration, which confirmed its regulatory effect on the microstructure. Heat treatment promoted uniform precipitation of γ′ and γ′′ phases on the GH4065A and IN718 sides, respectively, thereby increasing the volume fraction and average size of the γ′/γ′′ strengthening phases. After heat treatment, minor grain coarsening was observed in all the joint regions, along with a considerable reduction in local misorientation in the thermomechanically affected zone, indicating effective alleviation of stress concentration. Moreover, fine γ′/γ′′ phases precipitated in the heat-treated weld nugget zone, and dislocations that cut through these strengthening phases resulted in the formation of stacking faults, which further impeded dislocation motion and enhanced deformation resistance.