Registration of three-dimensional contrast-enhanced ultrasound fusion imaging (3DCEUS-FI) is time-consuming to obtain high success rate. To investigate the influence factors on registration success rate of 3DCEUS-FI. Water tank phantoms were made to obtain mimicked pre- and post- radiofrequency ablation three-dimensional contrast-enhanced ultrasound (3DCEUS) and CT images. Orthogonal trials were designed according to factors including size, depth, enhancement level of mimicked tumor, diameter and number of mimicked adjacent vessels. Mimicked pre- and post-RFA 3DCEUS images of 72 trials were fused to assess ablative margin (AM) by two radiologists. With CT images as standard, 3DCEUS-FI accuracy was considered as the consistency of AM evaluation. The inter-observer agreement and the influence factors on registration success rates were analyzed. The intraclass correlation coefficient (ICC) for the consistency of AM evaluation between CT and 3DCEUS-FI in x-axis, y-axis or z-axis was 0.840∼0.948 (P < 0.001). The ICC for inter-observer agreement was 0.840∼0.948 (P < 0.001). The success rates of registration within mimicked vessels with diameter of 2 mm were significantly lower than those with diameter of 3 mm and 4 mm. The mimicked AM measured by 3DCEUS-FI had high accuracy and inter-observer agreement. Diameter of the mimicked adjacent vessels was significantly related to success rate of registration.