Objectives. To investigate the accuracy of intraoperative frozen section (FS) diagnosis for predicting the permanent section (PS) diagnosis of mucinous ovarian tumors and evaluate the factors affecting the diagnostic discordance. Methods. This retrospective cohort study was performed in Tianjin Medical University General Hospital. All women who underwent mucinous ovarian tumor (MOT) surgery with FS between January 2011 and December 2022 were identified. Clinical and pathologic data were extracted. Results. A total of 180 women were included, of which 141 (78.33%) had diagnostic concordance between FS and PS, yielding a sensitivity of 83.43% and a positive predictive value (PPV) of 92.76%. Under-diagnosis and over-diagnosis occurred in 28 cases (15.56%) and 11 cases (6.11%). Tumor size > 13cm (OR 3.79, 95% CI 1.12-12.73) was an independent risk factor for under-diagnosis, and tumor size ≤ 13cm (OR 16.78, 95% CI 0.01-0.49), laparoscopic surgery (OR 0.14, 95% CI 0.02-0.92), the combination of other tumor components (including serous, Brenner tumor, and chocolate cyst; OR 7.00, 95% CI 1.19-41.12) were independently associated with over-diagnosis. The Kaplan-Meier survival curves and the log-rank test showed no significant difference between misdiagnosed and accurately diagnosed patients (all P > 0.05). Conclusion. Intraoperative frozen pathology of MOT is problematic for under- and overdiagnosis. The incorrect diagnosis of FS was related to determining the extent of surgery but had no impact on the patients’ long-term recurrence and survival outcomes. Surgeons need to obtain material accurately and enhance communication with pathologists during the operation to improve the accuracy of FS diagnosis.