Objective The clinical value of different scanning sequence of magnetic resonance imaging (MRI) in the diagnosis of anal fistula was analyzed. Methods A retrospective analysis of our hospital after surgery confirmed 30 cases of anal fistula patients, the patients were examined by MRI scanning sequence: FSE T1WI scan and enhanced scan, fast inversion recovery sequence (T2 fs FRFSE) and three-dimensional fast low angle shot imaging scan and enhanced image subtraction (3D-FSPGR) analysis and comparison of 3 kinds of sequence, then analyzed and compared the diagnostic value of the 3 sequences. Results A total of 43 different types of anal fistula were found in 30 patients. 43 lesions were external anal fistula fistula, anal fistula and accurate display of T2 fs FRFSE 18 (41.86%), FSE enhanced T1W accurately display the external anal fistulas in 25 (58.14%), 3D-FSPGR accurately displayed outside the anal fistula fistulas in 40 (93.02%), of which 3D-FSPGR of anal fistula significant accuracy rate was significantly higher than that of T2 fs FRFSE and FSE T1WI (P<0.05). T2 fs FRFSE accurately showed 10 lesions(35.71%) and 10 FSE (T1W) enhancement of fistula in the anal fistula, and 14 lesions(50.00%) of the fistula in the anal fistula. The 3D-FSPGR accurately showed 23 lesions(82.14%) of the fistula in the anal fistula, and the significant accuracy rate of 3D-FSPGR for the anal fistula was significantly higher than that of T2 fs FRFSE and FSE T1WI (P<0.05). T2 fs FRFSE accurately display the fistula 29 branches(56.86%), FSE enhanced T1W accurately display the fistula 34 branches (66.66%), 3D-FSPGR accurately display the fistula 45 branches (88.23%), of which 3D-FSPGR of branch fistula significant accuracy was significantly higher than that of T2 fs FRFSE and FSE T1WI (P<0.05). Conclusion 3D-FSPGR sequence is a sensitive method for preoperative diagnosis of anal fistula. It can improve the display rate of internal fistula,external fistula and anal fistula. Combined with other scanning sequences, we can get a more clear preoperative diagnostic result.