The objective of this study was to develop robust carbon fiber/epoxy (CF/epoxy)-carbon fiber/polyetherimide (CF/PEI) hybrid joint upon an ultrasonic welding process. The co-curing of a PEI coupling layer (CL) on the surface of the CF/epoxy composite makes it “meltable and weldable”. The CF/epoxy was then ultrasonically welded with the CF/PEI using different combinations of energy director (ED) and CL thicknesses. The results showed that high-quality welding line could be obtained by carrying out coupling-optimization to the thicknesses of the EDs and CLs using an optimal welding displacement. For example, a largest lap-shear strength (LSS) of 35.3 MPa was achieved when both of the ED and CL possessed an optimal thickness of 175 μm. In this case, a cohesive failure within either the CF/PEI or the CF/epoxy substrate took place during the single-lap shear test of the hybrid joints. Predictably, this study provides a promising strategy for the production of high-performance hybrid composite joints upon tailoring the thicknesses of the EDs and the CLs for the ultrasonic welding process.