Due to the large difference in physical and chemical properties between the substrate and the cladding material, the welding of composite materials is much more difficult than that of single materials. In our work, S32304/Q390C composite material was considered as the research object. By adjusting the welding parameters, two kinds of joint geometry were obtained, namely, the transition layer weld lower (joint A) and higher the composite material interface (joint B). We studied the influence of the transition layer weld on the microstructure and properties of welded joints. The microstructure of the transition layer weld, the distribution of elements, the Schmidt factor of the interface between the transition layer and base layer weld, and the tensile strength of the joint were evaluated. The results show that with the increase of welding heat input, the microstructure of the transition layer weld changes from austenite and skeleton ferrite to austenite and lathy ferrite and austenite and acicular ferrite, while ferrite grows towards the weld center, showing a dendritic shape and a local network structure. At the side of the base layer weld of the interface between the transition and the base layer weld, the thickness of the low-carbon-content layer increased from 100 μm to 150 μm. Iron, chromium, and nickel elements on both sides of the interface were diffused, and the thickness of the diffusion layer increased from 3 μm to 10 μm. The tensile strength values of joints A and B were 648 MPa and 668 MPa, respectively, and the Schmidt factor values were 0.446 and 0.454, respectively. Combination with the analysis of the fracture morphology showed that when the transition layer weld was higher than the interface of the composite plate, the joint had better plastic deformation ability and higher tensile strength.