Objective To explore the value of multi-disciplinary team (MDT) for fertility preservation in patients with borderline ovarian tumor (BOT). Methods BOT patients who underwent MDT at West China Second University Hospital of Sichuan University between January 2020 and December 2022 were selected as the MDT group, while BOT patients who underwent surgery but did not undergo MDT during the same period were selected as the control group in a 1∶2 histological ratio. The clinical case data of two groups were retrospectively analyzed. The fertility assessment, implementation of fertility protection measures, and reproductive outcomes of two groups of patients were compared. Results A total of 24 patients were included in the MDT group, while 48 patients were included in the control group. There was no statistically significant difference in age of onset, marital status, preoperative carbohydrate antigen 199, carbohydrate antigen 125, surgical pathway, and International Federation of Gynecology and Obstetrics staging between the two groups of patients (P>0.05). The proportion of bilateral tumor involvement in the MDT group during the first surgery was higher than that in the control group (50.0% vs. 22.9%, P<0.05). In terms of fertility assessment, there was no statistically significant difference in the proportion of patients who underwent preoperative measurement of anti-Müllerian hormone between the two groups (P>0.05). The proportion of patients who underwent postoperative measurement of anti-Müllerian hormone in the MDT group was higher than that in the control group (100.0% vs. 37.5%, P<0.05). The proportion of patients in the MDT group who took fertility protection measures was higher than that in the control group (62.5% vs. 29.2%, P<0.05). There was no statistically significant difference in the proportion of successful pregnancies between the two groups of patients who were married (28.6% vs. 25.9%, P>0.05). Conclusion MDT is beneficial for improving the fertility assessment rate of BOT patients of childbearing age, providing personalized treatment plans, and taking timely measures to protect their fertility.