Objective To evaluate the accuracy of diffusion weighted imaging (DWI) combined with generic sequence in complex anal fistula and to discuss the application value of DWI in complex anal fistula. Methods 30 cases of patients who were confirmed with complex anal fistula were given MRI before operation. Scan sequences included axial T1WI, T2WI and fat sequence T2WI, and coronal and sagittal fat sequence T2WI and DWI. With surgical results as the standard, conventional sequences and conventional sequences + DWI were compared for anal fistula, internal opening and abscess. Results For 30 cases of patients with anal fistula, sensitivity and positive predict value of MR conventional sequences were 81.4%(38/43) and 89.7%(35/39) respectively for internal opening; 90.2%(37/41) and 86.0%(37/43) for anal fistula; 91.6%(11/12) and 100%(11/11) for abscess. Sensitivity and positive predict value of MR conventional sequences + DWI were 95.3%(41/43) and 95.3%(41/43) for internal opening; 92.7%(38/41) and 97.4% (38/39) for anal fistula; 100%(12/12) and 100%(12/12) for abscess. In comparison of two kinds of diagnostic methods, conventional sequences + DWI had better diagnostic results on anal fistula than conventional sequences, and the sensitivity for internal opening was of statistical difference (P<0.05). Conclusions MRI + DWI shows higher clinical application value for internal opening and canal of anal fistula and abscess, which can be used as a conventional preoperative examination.