Objective: To establish an animal model with malignant tumor in the skull base-infratemporal region , and to explore the role of iodine staining technique in identifying tumor tissues with Micro-CT data . Methods: Sedation anesthesia was carried out on 12 BABL/c nude mice using inhaled isoflurane, and then WSU-HN6 cells that cultured and immortalized from human tongue squamous cell carcinoma were injected into the right infratemporal fossa via the submandibular area. The procedure was carried out under ultrasonographic guidance. The nude mice were sacrificed after 3 weeks observation. The head specimens were fixed and scanned by Micro-CT, and repeated scans were performed after staining with 3.75% compound iodine solution. Following decalcification in 20% EDTA for 2-4 weeks, the head specimens were embedded and sectioned. Hematoxylin and eosin staining and Pan-Keratin immunohistochemical staining were carried out. Bright-field microscopy and stereomicroscopy were used to visualize. The Micro-CT data were analyzed using iPlan software (Brainlab). Results: Non-traumatic ultrasonography was used to guide HN-6 cells injection and confirm skull-base tumor formation in all the animals. Ultrasonographic guidance reduced the risk of cervical vessel injury when transferring tumor cells into the skull base space. An obvious asymmetrical appearance was detected via ultrasonography 3 weeks after tumor cell injection. The Micro-CT analysis showed that the bone was obviously damaged on the right side of the skull base, but the soft tissue image was unrecognizable. After four days staining with compound iodine solution, the morphology of the tumor and surrounding soft tissue could be clearly identified. Hematoxylin and eosin staining showed the tumor formation of the right infratemporal fossa region accompanied by bone destruction. Human keratin immunohistochemical staining showed that the tumor tissue originated from human squamous cell carcinoma, and the polynuclear osteoclasts could be seen at the margin of the skull base bone resorption. Conclusion: The animal model with malignant tumor in the skull base-infratemporal region could be successfully established via submandibular injection under ultrasound-guidance. Bone changes of the skull were easily observed on Micro-CT, but the tumor counter was not able to be distinguished from surrounding soft tissue. The 3.75% compound iodine staining of the head specimen could help discern the tumor and surrounding soft tissue in more details.