Microstructural evolution of the zirconium alloy deformed at a strain rate of about 1000 s-1 was investigated. Four different strain levels of the zirconium alloy subjected to dynamic compression were designed by several-times impacting at almost the same strain rate. The results show that abundant low angle boundaries at different strain levels were observed in the deformed microstructures, and the quantity and density of low angle boundary increase dramatically with the strain increasing. Besides low angle boundaries and high angle boundaries observed in grain boundary maps, the twin boundaries including the tensile twins {10 2}, {11 1} and compressive twins {11 2} were distinguished at different strain levels, and most twin boundaries were indexed as {10 2} twins. With the stain increasing, the twin boundary density in the deformed microstructures increases indistinctively. Based on the characterization of the deformed microstructures at the different strain levels, the deformation and evolution processes of the zirconium alloy subjected to dynamic loading were proposed. Microhardness measurements show that the microhardness in the impacted specimens increases gradually with the strain increasing, which should be associated with the strain hardening caused by the tangled dislocation.