Krukenberg tumor originated from stomach in female patients is common in clinical practice, but it is still uncertain whether surgical resection of ovarian metastases could improve the outcome. Some studies suggested that a certain group of patients could benefit from the resection of ovarian metastases. However, conclusions were different between studies and there was no data to illustrate if certain molecular markers were associated with patients' survival. In this study, we analyzed the effects of resection of ovarian metastases, and investigated prognostic factors in 133 patients with ovarian metastases originated from stomach. Furthermore, we examined the expression of some cancer stem cells (CSCs) markers or related molecules in 64 ovarian metastases specimens and analyzed the correlation between these molecules and patients' survival. We found that the median overall survival (mOS) of all 133 patients was 16 months, and "gastrectomy" and "without ascites" were two independent prognostic factors associated with longer survival. The mOS of the patients with gastrectomy was longer than that of patients had not undergone gastrectomy (19 vs. 9 months, p = 0.048). Patients without ascites survived longer than those with ascites (mOS: 21 vs. 13 months, p = 0.008). We also found that Sox2, CD44 or CD133 positive expression in ovarian metastases were risk factors correlated with poor survival, and Sox2 expression was an independent prognostic indicator. These results suggested that ovarian metastasectomy might help to prolong the survivor of some patients with Krukenberg tumor originated from stomach. Patients without ascites, and with resected or resectable primary gastric cancer lesion could get benefit from and be potential candidate for surgical treatment. The expression of Sox2 might serve as a prognostic indicator for predicting patients' survival and be helpful for selecting patients in future.