We have demonstrated that the incorporation of sulfated galactose acid (sulf‐Gal) into thrombin‐binding‐aptamer (TBA)‐conjugated gold nanoparticles (TBA–AuNPs) enables highly effective inhibition of thrombin activity toward fibrinogen. AuNP bioconjugates (TBA15/TBA29/sulf‐Gal–AuNPs) were prepared from 13 nm AuNPs, 15‐mer thrombin‐binding aptamer (TBA15), 29‐mer thrombin‐binding aptamer (TBA29), and sulf‐Gal. The numbers of TBA and sulf‐Gal molecules per AuNP proved to have a strong impact on inhibitory potency. The best results were observed for 15‐TBA15/TBA29/sulf‐Gal–AuNPs (with 15 TBA15 and 15 TBA29 molecules per AuNP), which, because of their particularly flexible conformation and multivalency, exhibited ultrahigh binding affinity toward thrombin (Kd=3.4×10−12 M) and thus extremely high anticoagulant (inhibitory) potency. Compared to the case without inhibitors (the “normal” value), their measured thrombin clotting time (TCT) was 91 times longer, whereas for TBA15 alone it was only 7.2 times longer. Their anticoagulant activity was suppressed by TBA‐complementary‐sequence (cTBA)‐modified AuNPs (cTBA15/cTBA29–AuNPs) at a rate that was 20 times faster than that of free cTBA15/cTBA29. Thus, easily prepared, low‐cost, multivalent AuNPs show great potential for biomedical control of blood clotting.