Objective: Occlusal alteration due to tooth loss may cause overload of masticatory muscle and promote muscle dysfunction. This study explored the feasibility of using functional magnetic resonance imaging (fMRI) to evaluate muscle dysfunction in an established unilateral exodontia animal model. Methods: 6 rabbits were extracted right maxillary molars. T2 mapping, T2* mapping and Iterative Decomposition of water and fat with Echo Asymmetry and Least Square Estimation (IDEAL-IQ) were performed one day before extraction and every 2 weeks (2th similar to 12th week) after extraction. The T2 and T2* values and fat fraction (FF) of bilateral temporal muscle (TM), masseter muscle (MM) and medial pterygoid muscle (MPM) were measured and compared between the extraction side and the contralateral side. Parameters of three monitoring time points (0th, 6th, 12th week) were also analyzed. Results: T2 values of MM on extraction side were significantly higher than those of contralateral side-from fourth week to 12th week after extraction (p < 0.05). T2 values of MM and MPM on extraction side and TM on contralateral side were significantly higher in 12th week than those in 0th week (p < 0.05). And FF of bilateral MM was significantly higher in 12th week than those in 0th week (p < 0.05). T2* value showed no significant difference between extraction side and contralateral side and also at above three time points. Conclusion: T2 and T2* value and FF can be used as indicators of masticatory muscle dysfunction. fMRI is expected to be a non-invasive method for in vivo and real-time evaluation of masticatory muscle functional abnormality.