The microstructure and the second phases in the annealed Zr-Nb-Cu alloy were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The crystal structure of the second phases was determined by selected area electron diffraction (SAD) pattern, and the quantitative analysis of second phases was preformed using TEM with energy dispersion spectroscopy (EDS). Results show that there are two kinds of second phases in the Zr-Nb-Cu alloy. The first one is β-Nb with a bcc structure, small size and a dispersive distribution in the grains, and the second one is Zr2Cu precipitates with a tetragonal structure, big size and a distribution on the grain boundary.