We investigated the reliability of assessing a positional relationship between the inferior alveolar nerve (IAN) and mandibular third molar (MTM) based on CBCT, 3D-DESS MRI, and CBCT/MRI image fusion. Furthermore, we evaluated qualitative parameters such as inflammatory processes and imaging fusion patterns. Therefore, two raters prospectively assessed in 19 patients with high-risk MTM surgery cases several parameters for technical image quality and diagnostic ability using modified Likert rating scales. Inter- and intra-reader agreement was evaluated by performing weighted kappa analysis. The inter- and intra-reader agreement for the positional relationship was moderate (κ = 0.566, κ = 0.577). Regarding the detectability of inflammatory processes, the agreement was substantial (κ = 0.66, κ = 0.668), with MRI providing a superior diagnostic benefit regarding early inflammation detection. Independent of the readers' experience, the agreement of judgment in 3D-DESS MRI was adequate. Black bone MRI sequences such as 3D-DESS MRI providing highly confidential preoperative assessment in MTM surgery have no significant limitations in diagnostic information. With improved cost and time efficiency, dental MRI has the potential to establish itself as a valid alternative in high-risk cases compared to CBCT in future clinical routine.