Objective: To compare the clinicopathological features and chemotherapy response of ovarian clear cell carcinoma (CCC) and endometrioid carcinoma (EC) associated with endometriosis or not. Methods: This was a retrospective study of 128 patients diagnosed with CCC and EC from 2002 to 2017. Clinicopathological features and chemotherapy response were analyzed. Results:There were 34 women with endometriosis-associated ovarian cancer (EAOC) and 94 with non-endometriosis associated ovarian cancer (non-EAOC) according to Sampson's and Scott's criteria. The mean diagnosis age in the EAOC group was 48.65 vs. 54.39 years in non-EAOC (p = 0.002). Compared with non-EAOC, the EAOC patients were more likely to have an earlier menarche age (13 vs. 14 years, p = 0.001), a higher incidence of infertility (26.47% vs. 10.64%, p = 0.026), and an earlier stage tumor (91.18% vs. 73.40% in stages I-II, p = 0.032). At a median follow-up time of 32.9 months, overall survival among patients with EAOC was significantly longer (109.8 vs. 47.4 months, p = 0.007). Association with endometriosis (p = 0.033) was the significant favorable prognostic factors associated with survival. However, stratifying by stage, the overall survival advantage of EAOC was not significant. Although EAOC had a better prognosis, no difference was observed in chemotherapy response between the two groups (p = 0.535). Conclusions: The EAOC patients were often diagnosed at a younger age, an earlier stage, and related to nulliparity and infertility. Patients with EAOC had a better prognosis than non-EAOC, early stage rather than association with endometriosis may be the driver of survival.