Objective To summarize the occurrence of anal fistula in Crohn disease (CDAF) accompanying with rectal stenosis and analyze its influencing factors. Meanwhile to explore the effect of modified anal sphincter retention hang line for treatment of CDAF. Methods The CDAF patients admitted to the Third People’s Hospital of Bengbu from January 2019 to June 2021 were retrospectively collected, who were treated with modified anal sphincter retention hang line. Meanwhile the multiple logistic regression analysis was used to identify the risk factors for preoperative accompanying with rectal stenosis and which were used to establish a decision tree model using Chi squared automatic interaction detection method. Results A total of 234 patients with CDAF were collected, and the incidence of preoperative accompanying rectal stenosis was 22.2% (52/234). The multivariate logistic regression analysis found that the patients with preoperative proctitis, Montreal subtype B2, fistula located above the musculi levator ani (MLA), single and multiple fistulas, lymphocyte count (Lym) greater than 6.03×10⁹/L, platelet count (PLT) greater than 0.61×10⁹/L, erythrocyte sedimentation rate (ESR) greater than 39.11 mm/h, C-reactive protein (CRP) greater than 5.13 mg/L, and brain natriuretic peptide (BNP) greater than 313.26 ng/L had higher probability of preoperative accompanying rectal stenosis (P<0.05). For the patients with or without preoperative rectal stenosis before surgery, the score of CD activity index and perianal CD activity index, and anal resting pressure all showed decreasing trends after treatment with the modified anal sphincter retention hang line, and the anal maximal contraction pressure showed a increasing trend as compared to before treatment. The decision tree consisted 18 nodes and 9 terminal nodes. The gain map of the decision tree model gradually increased from 0% to 100%; The index chart maintained a high level starting from 198% and then rapidly decreased to 100%. The area under the operating characteristic curve of the subjects was 0.852 [95%CI (0.821, 0.908)], with a sensitivity of 84.35% and a specificity of 82.33%. Conclusions The incidence of preoperative accompanying rectal stenosis in patients with CDAF is relatively higher. The effect of modified anal sphincter retention hang line for treatment of CDAF is better. For patients with preoperative rectal inflammation, Montreal subtype B2, fistula above the MLA, single and branching fistulas, and higher Lym, PLT, ESR, CRP, and BNP, attention should be paid to their preoperative accompanying rectal stenosis. The decision tree model based on these factors to distinguish whether preoperative accompanying rectal stenosis is better.