The problem of ovarian tumor differential diagnosis is solved using comprehensive ultrasound examination at different levels of efficiency. However, ultrasound imaging is an operator-dependent technique due to subjective interpretation of results. The study was aimed to assess the ultrasound signs of benign and malignant ovarian germ cell tumors (OGCTs) in pregnant women in order to determine the feasibility of surgical treatment and chemotherapy. The study was carried out using the logistic regression models. A group of 199 pregnant women with benign and malignant OGCTs were enrolled. Of them, 183 patients had benign, and nine patients had malignant tumors. In order to assess menstrual function and fertility, seven pregnant women were enrolled, who had previously received treatment for malignant OGCTs. Pre-operative assessment results were compared with morphological assessment data. Organ-preserving surgical treatment was performed (unilateral adnexectomy); if necessary, the patients received cisplatin-based chemotherapy. Perinatal outcomes were assessed. The median observation time between the malignant OGCT detection and the end of the study was 66 months (12–240 months). It was found that comprehensive ultrasound examination and logistic regression models (sensitivity 100%, specificity 92.3%, overall accuracy 92.8%) enabled differential diagnosis of benign and malignant OGCTs. The number of unnecessary surgical procedures in patients with benign OGCTs was been limited, the pregnancy and childbirth outcomes were improved. Nine pregnant women received organ-preserving surgical treatment for malignant OGCTs, and three patients received chemotherapy after surgery, which allowed the patients to realize their reproductive potential.