Objective To analyze the application value of different MR sequences scanning in the clinical diagnosis of 30 cases with anal fistula. Methods Thirty patients with suspected anal fistula who were admitted to our hospital between March 2014 and September 2015 were given MR examination. Axial SE T1WI scan, coronal TIRM, axial T1WI enhanced scan and 3D-FLASH subtraction scan were performed. With the results of SE T1WI enhanced sequence as standard, the display rates of TIRM, SE T1WI scan and 3D-FLASH subtraction for external fistula, internal fistula and fistula branch in patients with anal fistula were statistically analyzed. Results Axial T1WI and T2WI of MRI scan for anal fistula canal showed ring-like low signal shadow and approximate muscular signal shadow in T1WI low signal ring and high signal in T2WI low signal ring. Coronary TIRM showed patchy high signal shadow down, and the relationship with sphincter is not clear; Sagittal scan showed fistula with tubular enhancement, small branches and surrounding soft tissue with small flocculent enhancement. The display of TIRM, SE T1WI scan and 3D-FLASH for internal fistula was poor. The display of 3D-FLASH for external fistula and fistula branch was superior to TIRM and SE T1WI scan. Conclusion 3D-FLASH sequence is of high sensitivity in diagnosis of anal fistula. Combination of axial 3D-FLASH and coronary TIRM sequence can improve the display rate of MRI for internal and external fistula of anal fistula, and shorten the examination time, especially for patients who can not tolerate anal fistula and stay in bed. It is of significant value in clinical application.