This study aimed to develop robust thermoplastic-to-thermoset composite joints upon an ultrasonic welding process. The carbon fiber/epoxy composite was topped with a layer of polyetherimide (PEI) film by a co-curing process, making it “weldable” with the carbon fiber/PEI composite. The effects of welding displacement and thickness of the energy director (ED) on the welding process of the epoxy-to-PEI hybrid composite joints were investigated. The experimental results demonstrated that an optimal welding displacement existed for the best welding quality, whose value depended on the ED thickness. Given a certain ED thickness, the lap-shear strength (LSS) of the hybrid joints increased to a maximum value and then decreased as the welding displacement increased. By optimizing the displacement and ED thickness, a maximum LSS of 39.4 MPa was obtained for the hybrid joints. In which case, the level of the defects within the welding line was minimized, and the joints failed cohesively within the composite substrates.