A quantum dot (QD) conjugate comprises a QD and a ligand conjugated with the QD, in which the ligand has at least one thiol and at least one other functional group. The QD conjugate may further comprise a bioactive agent covalently coupled to the ligand to form a bioactive agent-tagged QD conjugate. A method for preparing a QD conjugate comprises the steps of: (1) providing a solution comprising a QD encapsulated within a dendrimer; (2) adding into the solution a ligand; and (3) allowing an exchange between the ligand and the dendrimer for the QD to obtain a ligand-QD conjugate, in which the ligand is covalently conjugated to the surface of the QD. The method may further comprise the step of coupling the ligand-QD conjugate to a bioactive agent to obtain a bioactive agent-tagged ligand-QD conjugate.