Background: In this study, we investigate the incidence of venous thrombosis (VT), and evaluate the effectiveness and safety of 3 major thromboprophylaxes and the potential risk factors for VT in women undergoing surgery for a gynecological malignancy. Methods: We performed a randomized controlled trial of 307 patients undergoing laparoscopic surgery for gynecological malignancies at a single institution from January 2016 to October 2017. Patients were divided into 3 groups: one receiving a half dose of low-molecular-weight heparin sodium injection (FLUXUM, Alfa Wassermann, Italy) delivered by injection, one receiving a full dose of FLUXUM, and a third group receiving an Argatroban injection. Results: None of the patients in our study developed a pulmonary embolism, bleeding, or infectious complications. There were no statistical differences in the rate of deep venous thrombosis (DVT) (0%, 0%, and 2.38%) and the superficial venous thromboembolism (SVT) (15.66%, 8.97%, and 18.6%) among the 3 groups. None of the patients developed symptomatic VT. The effect of treatment on alanine aminotransferase and aspartate aminotransferase differed between the groups, with a minimal effect in the Argatroban group, and all 3 methods resulted in minimal impairment of renal function. Decreased hemoglobin, elevated levels of D-dimer, and prothrombin time were closely related to thrombogenesis. Conclusion: In conclusion, the incidence of postoperative thrombosis in gynecological malignancy among these Chinese people is not as low as we had originally presumed. Argatroban is not more effective than Parnaparin as a direct thrombin inhibitor, but it has less influence on liver function, which is beneficial for patients undergoing chemotherapy. Hemoglobin, D-dimer, and prothrombin time may be used to predict or detect thrombogenesis.