Objective To evaluate the value of magnetic resonanace imaging (MRI) on the diagnosis of complex anal fistula. Methods The preoperative digital examination and MRI with the phased-array coil were implemented for 22 patients who were clinically suspected with complex anal fistula. The final diagnosis were based on surgical findings. Outcomes of MRI and digital examination were compared with surgical results. Results Eighteen patients were diagnosed as complex anal fistula, 1 case of presacral cyst and 3 cases of chronic anorectal fistula combined with perianal mucinous adenocarcinoma. All the patients were correctly diagnosed by MRI, while the patients with presacral cyst and perinaal mucinous adenocarcinoma could not be diagnosed correctly by digital examination. According to the Parks classification, 3 patients suffered from transsphincteric fistula, 11 cases of supra-sphincteric and 5 cases of extra-sphincteric fistula. The diagnosis rates of the internal opening with digital examination and MRI were 33.3% and 72.2%, the rates of the primary tract were 83.3% and 100%, and the rates of the secondary extensions were 16.7% and 88.9%, respectively. The differences in detection of internal opening and secondary extensions between MRI and digital examination were significant (P=0.019, P=0.000), the difference in detection of primary tract was no significant (P=0.072). Conclusion MRI with the phased-array coil can develope the high accuracy in the diagnosis of complex anal fistulas, and reveal the relationship between anorectal sphincters and the complex fistula.