AimThe anticoagulation effect of warfarin is usually evaluated by percentage of time in therapeutic range (PTTR), which is negatively correlated with the risk of warfarin adverse reactions. This study aimed to explore the effects of genetic and nongenetic factors on anticoagulation efficacy of warfarin during different therapeutic range.MethodsWe conducted an observational retrospective study aiming at evaluating the impact of clinical and genetic factors on PTTR from initial to more than six months treatment. This analysis included patients with heart valve replace (HVR) surgery who underwent long-term or life-long time treatment with standard-dose warfarin for anticoagulation control in Second Xiangya Hospital. All patients were followed for at least 6 months. We genotyped single nucleotide polymorphisms inVKORC1andCYP2C9associated with altered warfarin dose requirements and tested their associations with PTTR.ResultsA total of 629 patients with intact clinical data and available genotype data were enrolled in this study, and only 38.63% patients achieved good anticoagulation control (PTTR > 0.6). Clinical factors, including male gender, older age, overweight, AVR surgery and stroke history, were associated with higher PTTR. Patients withVKORC1-1639AA genotype had significantly higher PTTR level compared with GA/GG genotype carriers only in the first month of treatment. Patients withCYP2C9*3 allele had higher PTTR compared withCYP2C9*1*1 carriers. Moreover, compared withVKORC1-1639 AG/GG carriers, INR > 4 was more likely to be present in patients with AA genotype. The frequency ofCYP2C9*1*3 in patients with INR > 4 was significantly higher than these without INR > 4.ConclusionWe confirmed the relevant factors of warfarin anticoagulation control, including genetic factors (VKORC1 -1639G > A and CYP2C9*3 polymorphisms) and clinical factors (male gender, older age, overweight, AVR surgery and stroke history), which could be helpful to individualize warfarin dosage and improve warfarin anticoagulation control during different treatment period.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12872-023-03321-9.