The electric pulse modification (EP, EPM) of liquid metal is a novel method for grain refinement. The structure of EP-modified Al-5%Cu melt was characterized by high-temperature X-ray diffractometry. The results show that the Cu-containing Al clusters remarkably increase in the EP-modified melt, furthermore, these clusters in that case tend to contract due to the decrease of relevant atomic radius and the co-ordination number. This kind of liquid-phase structure leads to a more homogeneous Cu-rich phase distribution in the final solidification structure. Differential scanning calorimetry (DSC) tests indicate that the solidification super-cooling degree of the EP-modified liquid phase is 2.36 times that of the unmodified. These facts suggest that the atom cluster changes in EP-modified Al-5%Cu melt would disagree with that by EPM model previously proposed in liquid pure metal.