An energy model for the melt of bulk metallic glass (BMG) with clusters was established, the Gibbs free energy and interfacial energy for the Zr-Al-Ni ternary alloy melt with Zr2Ni clusters were calculated, and the effects of the clusters on the Gibbs free energy, interfacial energy and nucleation rate were analyzed. The results showed that the existence of the clusters in the Zr-Al-Ni ternary alloy melt enables the Gibbs free energy to decrease in the composition range where bulk metallic glass forms easily, makes the interfacial energy increase and changes the distribution of the interfacial energy with the alloy composition. Because of the clusters in the melt, the Gibbs free energy of the Zr66Al8Ni26 alloy melt decreases about 0.3-1 kJ/mol and the interfacial energy between the melt and crystal nucleus increases about 0.016 J/m2. The nucleation rate of the undercooled Zr66Al8Ni26 alloy melt decreases evidently under the influence of the clusters on Gibbs free energy and the interfacial energy, and the maximum of the nucleation rate in the melt with the Zr2Ni clusters is only about 107 mol-1·s-1.