Objective To compare the ultrasonographic features between common anal fistula and Crohn's disease associated anal fistula in order to provide more information for clinical differential diagnosis. Methods The clinical data of West China Hospital from December 2010 to September 2020 were retrospectively analyzed. The adult patients diagnosed with Crohn's disease were included. All patients were complicated with anal fistula, totally 25 cases with 38 anal fistulas. Seventy five patients with 95 common anal fistulas were enrolled according to the ratio of 1:3 (Crohn's disease associated anal fistulas / common anal fistulas). Clinical information, ultrasonic data and other imaging results were collected. The ultrasonographic features were compared between the two groups, including rotation, width, fistula wall thickening sign, intrafistular abnormal echo, the relationship between the fistula and perianal sphincter, fistula classification, perianal abscess, blood flow signal, accordance with goodsall's law, etc. Results Compared with common anal fistulas, Crohn's disease associated anal fistulas were characterized by abscess, thickening of fistula wall, and fistula width≥3mm. While common anal fistulas were more in accordance with Goodsall's Law (P＜0.05). There was no significant difference between the two groups in the location, rotation, relationship between fistula and perianal sphincter, classification and blood flow signal (P＞0.05).Conclusion There are some differences between Crohn's disease associated anal fistula and common anal fistula in sonographic features. Crohn's disease associated anal fistula is more likely to be with thicker fistula wall, perianal abscess, and probably wider. The above features help to distinguish the two.