Neurovascular compression syndrome (NVCS), characterized by cranial nerve compression due to adjacent blood vessels at the root entry zone, frequently presents as trigeminal neuralgia (TN), hemifacial spasm (HFS), or glossopharyngeal neuralgia (GN). Despite its prevalence in NVCS assessment, Magnetic Resonance Tomographic Angiography (MRTA)'s limited sensitivity to small vessels and veins poses challenges. This study aims to refine vessel localization and surgical planning for NVCS patients using a novel 3D multimodal fusion imaging (MFI) technique incorporating computed tomography angiography and venography (CTA/CTV). A retrospective analysis was conducted on 76 patients who underwent MVD surgery and were diagnosed with single-site primary TN, HFS, or GN. Imaging was obtained from MRTA and CTA/CTV sequences, followed by image processing and 3D-MFI using FastSurfer and 3DSlicer. The CTA/CTV-3D-MFI showed higher sensitivity than MRTA-3D-MFI in predicting responsible vessels (98.6% vs. 94.6%) and NVC severity (98.6% vs. 90.8%). Kappa coefficients revealed strong agreement with MRTA-3D-MFI (0.855 for vessels, 0.835 for NVC severity) and excellent agreement with CTA/CTV-3D-MFI (0.951 for vessels, 0.952 for NVC). Resident neurosurgeons significantly preferred CTA/CTV-3D-MFI due to its better correlation with surgical reality, clearer depiction of surgical anatomy, and optimized visualization of approaches (p < 0.001). Implementing CTA/CTV-3D-MFI significantly enhanced diagnostic accuracy and surgical planning for NVCS, outperforming MRTA-3D-MFI in identifying responsible vessels and assessing NVC severity. This innovative imaging modality can potentially improve outcomes by guiding safer and more targeted surgeries, particularly in cases where MRTA may not adequately visualize crucial neurovascular structures.