We found some clear cell glands appeared in the endometrioid cysts (ECs) of the ovary (EC-CCG). To explore the clinicopathological features, molecular biological changes, and prognosis in EC-CCG and analyze the association with ovarian clear cell borderline tumors (CCBT) and clear cell carcinoma (CCC). We retrospectively examined 35 cases of EC-CCG, compared them to 13 cases of clear cell cystadenomas, 14 cases of CCBT, and 49 cases of CCC. We analyzed the differences in clinicopathological features and prognosis between the four groups. Data on clinicopathology and survival were gathered. Immunohistochemistry (IHC) was performed in all cases, and we analyzed the molecular changes of 2 cases of EC-CCG and 1 case of CCC by whole-exome sequencing (WES). EC-CCG shared some common clinicopathological features with CCBT: they occurred before menopause, had an elevated serum CA125 level in some cases, had an ovarian cystic mass on B-ultrasound, and had a risk of recurrence. Microscopically, both diseases were based on typical EC, and clear cell glands in the EC cyst wall were seen in varying numbers. Some cases of EC-CCG had IHC results similar to those of CCBT and CCC, with positive expression of HNF1β and NapsinA; decreased expression of ER, PR, and ARID1A; and increased expression of Ki67 (> 5%). WES results revealed that EC-CCG had mutations in TP53BP1, ZNF462, FN1, and FTL (which was also mutated in CCC). In summary, we found that clear cell glands appearing around EC in the ovary have an association with CCC.