Objective To investigate whether the individualized anticoagulation therapy based on CYP2C9 and VKORC1 gene is superior to empirical anticoagulation therapy after artificial heart valve replacement surgery in Uygur patients. Methods From December 2012 to December 2015, 210 Uygur patients who underwent artificial heart valve replacement surgery at the First Affiliated Hospital of Xinjiang Medical University were randomly assigned to a genetic anticoagulation therapy group (group A, n=106, 41 females and 65 males, aged 44.7±10.02 years) or an empirical anticoagulation therapy group (group B, n=104, 47 females and 57 males, aged 45.62±10.01 years) according to the random number table. CYP2C9 and VKORC1 genotypes were tested in the group A and then wafarin of administration in anticoagulation therapy was recommended. Patients in the group B were treated with conventional anticoagulation. Patients in both groups were followed up for 1 month and coagulation function was regularly tested. Results The percentage of patients with INR values of 1.8-2.5 after 4 weeks warfarin anticoagulation treatment in the group A was higher than that in the group B (47.1% vs. 32.7%, P=0.038). The rate of INR≥3.0 in the warfarin anticoagulation therapy period in the group A was lower than that in the group B (21.6% vs. 26.5%, P=0.411). The time to reach the standard INR value and the time to get maintenance dose were shorter in the group A compared with the group B (8.80±3.07 d vs. 9.26±2.09 d, P=0.031; 14.25±4.55 d vs. 15.33±1.85 d, P=0.032). Bleeding occured in one patient in the group A and three patients in the group B (P=0.293). Embolic events occured in three patients in the group A and five patients in the group B (P=0.436). Conclusion Compared with the empirical anticoagulation, the genetic anticoagulation based on wafarin dosing model can spend less time and make more patients to reach the standard INR value. However there is no significant difference between the two groups in the ratio of INR≥3.0, bleeding and embolic events in the warfarin anticoagulation therapy.