Surgical plugging to treat superior semicircular canal dehiscence (SCD) has been proven to impede the effect of the third mobile window, abating cochleovestibular symptoms. Knowledge of superior semicircular canal (SC)-plugging status has been proposed to serve as a guide for adjuvant treatment. Here, we investigated disturbances in the inner ear fluid space following SC plugging using a novel three-dimensional (3D) reconstruction-based method. This approach used a semi-automatic segmentation algorithm and a direct volume rendering method derived from conventional magnetic resonance images. The variable extents of filling defects at the sites of SC plugging and the positional relation of the defect to the ampulla and common crus were identified. The success group exhibited markedly reduced volumes following surgery, whereas the failure group displayed no changes in volume. These results indicate that the success or failure of SC plugging was related to 3D volume changes in the labyrinth fluid signal. Collectively, this study presents individualized SC-plugging statuses using a novel 3D reconstruction-based method and it facilitates future work regarding easy-to-measure 3D volume changes. This current technology also aids in the exploration of pathologic changes in various targets of interest.