Abstract: CdSe quantum dots (QDs) were synthesized in an organic system, in which paraffin and oleic acid acted as reducing and stabilizing reagent, respectively. Modified with 2-mercaptoacetic acid, the QDs were water-soluble which could be applied in bio-system. Their interactions between CdSe QDs and several proteins with different structures were studied. After conjugation with bovine serum albumin (BSA) and chymotrypsin, the fluorescence intensity of CdSe QDs was enhanced obviously and quenched after reacting with Cu/Zn-SOD. However, the fluorescence intensity of CdSe QDs was enhanced firstly, and then decreased with the increasing of reaction time with bovine hemoglobin. It embodied the coordinated effects of normal proteins and part of metal ions. The former could enhance its intensity, the latter could quench it.