Pathological analysis of ovarian cysts shows specific fluid characteristics that cannot be standardly evaluated on computer tomography (CT) examinations. This study aimed to assess the ovarian cysts’ fluid attenuation values on the native (Np), arterial (Ap), and venous (Vp) contrast phases of seventy patients with ovarian cysts who underwent CT examinations and were retrospectively included in this study. Patients were divided according to their final diagnosis into the benign group (n = 32) and malignant group (n = 38; of which 27 were primary and 11 were secondary lesions). Two radiologists measured the fluid attenuation values on each contrast phase, and the average values were used to discriminate between benign and malignant groups and primary tumors and metastases via univariate, multivariate, multiple regression, and receiver operating characteristics analyses. The Ap densities (p = 0.0002) were independently associated with malignant cysts. Based on the densities measured on all three phases, neoplastic lesions could be diagnosed with 89.47% sensitivity and 62.5% specificity. The Np densities (p = 0.0005) were able to identify metastases with 90.91% sensitivity and 70.37% specificity, while the combined densities of all three phases diagnosed secondary lesions with 72.73% sensitivity and 92.59% specificity. The ovarian cysts’ fluid densities could function as an adjuvant criterion to the classic CT evaluation of ovarian cysts.