Objective To observe the effect of sphincter preservation seton applied in complex anal fistulas treatment. Methods 122 cases of patients with complex anal fistulas treated from October 2010 to 2013 were selected and divided into A and B group randomly and equally. And sphincter preservation seton was applied in A group, while fistula resection applied in B group. The cure rate of short and long term, healing time and occurrence of sequel were compared. Results Standard cure was got in both groups, and there were no statistically significant difference between the cure rates and recurrence rates of short term in the 2 groups. Healing time in A group was (20.74±5.62) days, and (19.19±6.84) days in B group (P>0.05), and no statistically significant difference was between the 2 groups. Occurrence of sequel was 3.28% in A group, while 37.70% in B group, (χ²=14.182, P<0.05), and the occurrence of sequel in A group was much lower than that in B group. Conclusion Complex anal fistulas could be treated well by both sphincter preservation seton and fistula resection, and normal physiological function of anus could be better retained by sphincter preservation seton, and the superiority of reduction of postoperative sequelae was apparent by former surgical. It was worthy of clinical use.