As the first safety shield of the nuclear reactor, the microstructure of zirconium alloys is one of the most popular research focuses in the world, especially for secondary phases, hydrides and oxidation film. In this paper, the research progress about the effect of neutron irradiation on secondary phases and hydrides in zirconium alloys was summarized. In addition, the shortages in present research were found and some suggestions were given, such as obtain the evolvement rules under actual employ conditions by using microstructure analysis methods to investigate the secondary phases, hydrides and oxidation film in zirconium alloy under different neutron fluence. Furthermore, theoretic supports for optimizing and improving on zirconium cladding materials in China would be given by this research.