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We presented a homogeneous heparin-mediated fluorescence anisotropy (FA) assay of antithrombin (AT) based on long-lived luminescent polyethyleneimine capped Mn-doped ZnS (PEI-Mn-ZnS) QDs. The PEI-Mn-ZnS QDs with long lifetime luminescence at 585 nm displayed a very low background of FA value, which was very helpful for FA assaying of large molecules. The medium heparin was crucial for AT determination, and different heparin amounts resulted in different linear range of detection and sensitivity. For example, the limit of detection (LOD) of 0.9 nM AT with a detection linear range from 8.6 nM to 21.5 nM was found when the heparin concentration was 75 μM. The proposed method also exhibited high selectivity over the coexisting or related proteins such as human serum albumin and thrombin.