MRI is the primary image diagnosis of nasopharyngeal carcinoma (NPC) at the stage T or N. For diagnosis of NPC, the presence of skull-based invasion is an important indicator for grading. In the early tumor infiltration, tumor cells have invaded bone marrow without re-arrangement of trabecular and cortical bones. Routine MRI diagnosis depends on physician’s objectively visual determination without quantification and standardization. Our study showed that T1 and T2 values in patients with skull-based invasion of NPC were higher and lower than healthy volunteers, respectively. MAGiC imaging sequence could help physicians determine NPC with or without skull-based invasion.