ObjectiveTo evaluate the risk factors of isolated distal deep vein thrombosis (IDDVT) in the lower limbs by using a combination of Doppler ultrasound and thrombus molecular markers.MethodsA prospective cohort study was used. We selected 145 patients with deep vein thrombosis of the lower limbs. They were divided into the IDDVT group and the non‐IDDVT group. We compared the differences in Doppler ultrasound and biochemical indexes between the two groups. The independent influencing factors of IDDVT were analyzed using logistic regression, and we plotted the receiver operating characteristic (ROC) curve.ResultsWe compared 47 IDDVT cases diagnosed by DSA with 47 non‐IDDVT cases selected at random. The diameter of the common femoral vein (CFV) of the affected side, deep femoral vein, and the great saphenous vein, thickness of subcutaneous tissue, and serum D‐dimer (D‐D) and thrombin–antithrombin III complexes (TAT) were significantly higher in the IDDVT group than the non‐IDDVT group (P < .05). Logistic regression analysis showed that CFV diameter, subcutaneous tissue thickening, D‐D, and TAT were all independent risk factors for IDDVT (P < .05). The combined predictor had higher predictive sensitivity, specificity, and Youden's index (93.6, 87.2, and 0.808, respectively) than using thrombus molecular markers alone or Doppler ultrasound alone.ConclusionD‐D and TAT, the thrombosis molecular markers, CFV diameter, and thickening of subcutaneous tissue, as well as the Doppler ultrasound, all have their own independent effects on IDDVT. When Thrombosis molecular markers and Doppler ultrasound are used in combination, they can predict which patients are at high risk of IDDVT and help doctors in making clinical decisions pertaining to prevention and treatment.