Objective To observe the application value of three-dimensional imaging of contrast CT in preoperative diagnosis and treatment of anal fistula. Methods The clinical data of 42 patients with suspected anal fistula were retrospectively analyzed. All patients were given fistulography CT plain scan and three-dimensional reconstruction before operation. The diagnostic efficacy of three-dimensional imaging of contrast CT in the diagnosis of anal fistula was evaluated. Results The coincidence rate of classification diagnosis of anal fistula and surgical results in anorectal physical examination was significantly lower than that of the three-dimensional imaging of contrast CT and surgical results (59.52% vs 100%) (P<0.05). The coincidence rate of classification diagnosis of anal fistula and surgical results was 90.48% in three-dimensional imaging of contrast CT. The preoperative diagnostic accuracies of three-dimensional imaging of contrast CT on the internal fistula, branches and abscess were 63.89%, 89.47% and 100% respectively. Conclusion Three-dimensional imaging of contrast CT has good preoperative diagnosis effects on the types and classification of anal fistula and the internal fistula, branches and abscess. And it has important significance in guiding surgical treatment.