To investigate the microstructural evolution during high temperature oxidation, Cr-coated Zr-4 alloy specimens are prepared by multi-arc ion plating and high temperature oxidation tests are carried out under 1000 °C, 1100 °C and 1200 °C in air atmosphere. Cr2O3 layers are formed on the surface after high temperature oxidation test. However, the thickness of Cr2O3 layer does not depend monotonously on the oxidation temperature. The oxidation temperature increases from 1000 °C to 1100 °C, the thickness of Cr2O3 layer increases from 2.35 μm to 5.74 μm, while the thickness is only 4.1 μm when the oxidation temperature is 1200 °C. This is mainly due to the reduction of Cr2O3 to Cr, and oxygen diffuses into the substrate to form α-Zr. The oxidation weight gain for the three temperatures conforms to an exponential function, while the thickness of the Cr-Zr diffusion layers follows a linear relationship with the oxidation temperature. Regarding the Zr-4 alloy substrate, the Zr grains grow up and gradually change from elongated grain parallel to the interface to elongated grain along normal direction after high temperature oxidation. Moreover, different oxidation temperatures bring distinct recrystallization energy to Zr grains, and the defects and dislocations produced during the recrystallization of Zr grain are unequal. The kernel average misorientation values obtained from EBSD indicate that the overall density of defect and dislocation of Zr grains after high temperature oxidation under 1100 °C is higher than the other two temperatures, while Zr grains after high temperature oxidation under 1000 °C has the highest local density of defect and dislocation. The investigation in this study attempts to reveal the microstructure evolution of Cr coating and Zr-4 substrate during the high temperature oxidation. These results give some new perspectives on understanding the performance of Cr-coated Zr-4 alloy under high temperature environment.