Purpose The study is aimed to evaluate the potential effect of clinicopathologic and surgical factors on the prognosis and fertile outcomes in the patients with borderline ovarian tumors. Patients and Methods We performed a retrospective analysis involving BOT patients who had underwent surgical procedures in West China Second University Hospital from January 2008 to January 2015 . The disease-free survival (DFS) outcomes and potential prognostic factors were evaluated using Kaplan-Meier method and Cox regression analysis, respectively. Furthermore, the fertile outcomes were analyzed using Pearson Χ2 and Fish correlation test. Results A total of 448 patients were included with a median age of 37.1 years and a median follow-up time of 113 months. Forty-two (11.6%) recurrences with the mean recurrence interval 80.2 months and four (0.9%) deaths were observed. One hundred and eighteen (26.3%) patients were underwent staging surgery and the remaining 330 (73.7%) patents underwent unstaged surgery. A total of 233 patients undergoing fertility sparing surgery (FSS) attempted to conceive and 92 (39.48%) of them achieved pregnancy. No statistically significant difference of fertile outcomes were found between staging surgery group or not (P=0.691). In univariate analyse, staging surgery was obviously associated with DFS (HR=2.191 P=0.005), but was not an independent prognostic factor (p=0.600) for DFS on multivariate analysis. The multivariate Cox analysis revealed that advanced FIGO stage (≥stage II), positive ascites\pelvic washings and laparotomy approach were independent prognostic factors for DFS in overall patients, whereas advanced stage (≥stage II), laparotomy approach, cystectomy-included procedure, invasive implants and bilateral tumors were independent prognostic factors for DFS in patients undergoing FSS. In addition, laparoscopy approach had better prognosis than laparotomy in patients of early stage (stage I) with fertility desire. Conclusion Patients with BOT fail to benefit from surgical staging in prognosis and fertile outcomes. Laparoscopy will be recommended to patients of stage I with fertility desire. Patients with fertility desire at advanced stage (≥stage II), invasive implants and bilateral tumors should pay more attention to the risk of recurrence and choose FSS carefully.