Objective: To investigate the predictive value of preoperative CT enterography (CTE) in evaluating the inflammatory activity of Crohn’s disease (CD) and early anastomotic recurrence (EAR) after primary enterectomy. Methods: 70 patients with CD who underwent initial intestinal resection were selected as research subjects and divided into an active group (n = 42) and a remission group (n = 28) based on inflammatory activity. Endoscopic examination was performed within 6 months after surgery; according to whether EAR occurred, patients were further classified into a recurrence group (n = 16) and a non-recurrence group (n = 54). Clinical characteristics, CTE signs, and SES-CD scores were compared between the different inflammatory activity groups and between the recurrence and non-recurrence groups, respectively. Receiver operating characteristic (ROC) curves were drawn to analyze the efficiency of CTE signs in evaluating CD inflammatory activity and predicting EAR after primary enterectomy in CD patients. Results: The thickness of the intestinal wall, CT value of the intestinal mucosa in the venous phase, ΔCT value, intestinal stenosis rate, mesenteric lymph node enlargement rate, mesenteric fibrofatty hyperplasia rate, comb sign rate, abscess/fistula rate, and the probability of intestinal wall stratified enhancement type A and type B were all significantly higher in the active group than in the remission group (P < 0.05). In the recurrence group, the thickness of the intestinal wall, CT value of the intestinal mucosa in the venous phase, ΔCT value, and rates of mesenteric lymph node enlargement, mesenteric fibrofatty hyperplasia, and abscess/fistula were significantly higher than those in the non-recurrence group (P < 0.05). ROC curve analysis indicated that the area under the curve (AUC) of the combination of CTE signs in predicting inflammatory activity of CD was 0.967. The AUC for predicting EAR after primary enterectomy in CD patients was 0.977, which was significantly higher than the AUC of any single CTE sign (P < 0.05). Conclusion: CTE signs and a comprehensive CTE-based scoring system have high value in the combined evaluation of inflammatory activity in Crohn’s disease and demonstrate excellent predictive performance for early anastomotic recurrence after primary enterectomy in CD patients.