Ultrasonic welding of thermoplastics is widely applied in automobile and aerospace industries. Increasing the weld area and avoiding thermal decomposition are contradictory factors in improving strength of ultrasonically welded polymers. In this study, relations among the loss modulus of carbon-fiber-reinforced polyamide 66 composite (CF/PA 66), time for obtaining stable weld area, and time for CF/PA 66 decomposition are investigated systematically. Then, a double-pulse ultrasonic welding process (DPUW) is proposed, and the temperature evolutions, morphologies and structures of fractured surfaces, and tensile and fatigue properties of the DPUWed joints are measured and assessed. Experimental results show the optimal welding parameters for DPUW include a weld time of 2.1 s for the first pulse, a cooling time of 12 s, and a weld time of 1.5 s for the second pulse. The DPUW process enlarged the weld area while avoided decomposition of CF/PA 66 under appropriate welding parameters. Compared to the single-pulse welded joint, the peak load, weld area, and endurance limit of the DPUWed joint increased by about 15%, 23% and 59%, respectively. DPUW also decreases the variance in strengths of the joints.