Background: Ovarian clear cell carcinoma (OCCC) is the most common pathological type of ovarian cancer associated with endometriosis. The effect of endometriosis on the prognosis of ovarian clear cell carcinoma remains controversial. This study aimed to investigate the clinical features and prognostic factors of pure OCCC. Methods: This single-center retrospective study analyzed 136 cases of pure OCCC after surgical treatment between 2010 and 2019. Patients were divided into two groups according to whether the pathologically relevant background lesion was ovarian endometriosis. Clinical data were compared between the groups. The Kaplan–Meier test and Cox regression analysis determined prognostic factors for survival. The primary outcome measure of the study was the duration of survival. Results: 83 (61%) participants had ovarian endometriosis of pure OCCC. Patients with ovarian endometriosis were significantly younger (50.55 \pm 8.25 vs. 54.57 \pm 6.71 years, p = 0.004), with lower deep venous thrombosis incidence and lower mortality and recurrence rates. Univariate analysis showed preoperative serum cancer antigen 125 (CA-125) level, endometriosis, tumor size, ascites, International Federation of Gynecology and Obstetrics (FIGO) stage, and chemotherapy resistance were significant prognostic factors. In particular, patients with endometriosis have an improved prognosis (p 0.05). Multivariate analysis showed that chemotherapy resistance and FIGO stage were significantly associated with progression-free survival (PFS) and overall survival (OS) (p 0.001). Conclusions: Pure OCCC with endometriosis has unique clinical features. However, endometriosis has no independent prognostic significance. Our findings indicate that FIGO stage and chemotherapy resistance affect prognosis.