With growing emphasis on energy saving and emission reduction, lightweight structures have become a key development focus in vehicle manufacturing. Magnesium and aluminum alloys, as lightweight materials with excellent properties, have broad applications in aerospace, automobile manufacturing, 3C products, and other fields. Mg/Al composite components can fully leverage the advantages of both alloys. Therefore, achieving high-quality and high-efficiency joints of Mg/Al dissimilar alloys has become a critical challenge in the manufacturing industry. Among the important structural types of Mg/Al thin-plate dissimilar welded joints, lap joints have attracted considerable attention. Friction stir welding (FSW), a solid-state joining process, offers distinct advantages for producing high-quality, defect-free Mg/Al joints. Ultrasonic-assisted FSW can further broaden the process window and enhance joint strength. However, the mechanism by which ultrasound influences joint formation during welding remains unclear. In this study, ultrasonic vibration-enhanced friction stir lap welding experiments were conducted on magnesium alloy and aluminum alloy sheets. The optimal process parameters were determined to be a rotation speed of 800 r/min and a welding speed of 90 mm/min. During welding, the keyhole region of the lap joint was subjected to a “sudden stop + freezing” treatment. Material flow behavior was characterized on vertical cross-sections at various angles around the keyhole, on horizontal cross-sections, near the magnesium alloy side, and along the weld centerline across the keyhole. The influence of ultrasonic vibration on the mechanical properties of the lap joints was also evaluated. The results show that introducing ultrasonic vibration during FSW enhanced both the tensile shear strength and the effective sheet thickness of the Mg/Al lap joints. Furthermore, ultrasonic vibration increased the volume of material driven by the tool, promoting enhanced material flow and mixing. During joint formation, the grain size distribution around the keyhole on the magnesium alloy side became more uniform, and the grains behind the keyhole underwent a significantly higher degree of recrystallization.