The utilization of a microwave (MW) hybrid heat source for the fabrication of dissimilar joints is now experiencing significant growth in the domain of advanced welding. The heat source has the ability to evenly disperse heat over a given space and selectively focus on particular areas. This solution is economically efficient and sustainable, providing advantages to numerous sectors. Researchers have utilized microwave hybrid heating to weld engineering materials that are similar or different. Nevertheless, the process of joining and characterizing materials that are not compatible, such as Inconel 625 and SS 304, using the MW heat supply has not been given much consideration. Furthermore, the potential uses of the weldments have not been adequately discovered. This study used the SMHH technique, i.e., selective microwave hybrid heating, to investigate the impact of an interfacial gap, type of susceptor, and separator thickness on the joining of Inconel 625/SS 304 alloys. In SMHH, Ni-based powder is employed as an interfacial material. The process parameters used are interfacial gap (0.25, 0.5, 1 mm), susceptor (SiC powder, stone charcoal, Charcoal) to raise the preliminary temperature and separator of thickness (0.5, 0.75, 1 mm) to avoid the mixing of filler and susceptor respectively. The experimental results show that the combination of 0.25 mm interfacial gap, SiC as susceptor, and 0.5 mm graphite sheet provide the optimal tensile strength 422 MPa. The interfacial gap between the specimens was found to be influenced significantly by the UTS of the joint specimen, followed by using SiC susceptor. The SiC susceptor, owing to its high loss tangent, absorbed the microwave rapidly and, thus, increased the temperature at the joint interface, which resulted in favorable tensile strength. Further, the XRD results of the joints reveal the presence carbides and intermetallic like Ni8Nb, NbC, Cr23C6, Ni3Cr2, Cr7C3, Fe2.50Ti0.5O4, and Fe3Ni2. Due to the existence of brittle carbide and intermetallic, the weld zone was found to fracture, i.e., a combined mode of fracture occurs, which is ascertained by SEM.