In fetoscopic tracheal occlusion (FETO) surgery, the localization of a flexible tool has an important role in easing high demands for surgeons. In this paper, a point-based 3D ultrasound (US) calibration system is proposed for localizing the surgical tool, based on real-time 3D US images, an electromagnetic (EM) tracking device, and a novel cones' phantom. A 3D US probe attached with an EM sensor is used to acquire the 3D US images of the surgical tool; meanwhile, an EM transmitter is fixed at a certain point in the environment as the origin of the world coordinate system. From these 3D US images, the skeleton of the surgical tool is extracted, and 15 labeled points along the surgical tool are then distinguished, whose coordinates in the world coordinate system are calculated by the proposed 3D US calibration system. The results demonstrate that our proposed approach achieves high localization accuracy, i.e. the average TRE of 1.99 ± 0.49 mm and the maximum TRE of 2.61 ± 0.49 mm, which satisfy the requirement of the FETO surgery: less than 3.85 mm.