The amount of heat input during welding impacts the weld’s thermal and mechanical behavior and the joint’s properties. The current study involved conducting AA 6061 and AZ31B Mg dissimilar welding, using friction stir lap welding (FSLW) and ultrasonic vibration-enhanced FSLW (UVeFSLW). The comparison and analysis of the welding load, the weld’s macro-microstructure, intermetallic compounds (IMCs), and joint properties were conducted by adjusting the process parameters. The study also examined the effect of ultrasonic vibration (UV) variations on welding heat input. The study demonstrated that it is possible to reduce the welding load by employing UV. Moreover, this impact becomes more pronounced as the welding heat input decreases. Additionally, the material flow in the weld, the width of the weld nugget zone, and the continuous IMC layer are significantly influenced by ultrasonic vibration, irrespective of the heat input during welding. However, the impact on large areas of irregular IMCs or eutectic structures is relatively small. Furthermore, achieving better joint properties becomes more feasible when a higher welding speed is employed for the Al alloy placed on top. Specifically, the impact of UV becomes more evident at higher welding speeds (≥220 mm/min).