Understanding the mechanism of the formation and evolution of shear band is important for improving and designing the mechanical properties of amorphous alloys. Molecular dynamics simulation study on the uniaxial compression of amorphous Ca65Mg15Zn20 alloy was performed in this work. The hidden correlation between the microstructure and evolution of shear band was revealed by a tracing method based on our previously proposed largest standard cluster analysis method. Results indicated that the topologically close-packed clusters are intrinsic characteristic structures of metallic glasses that closely related with the deformation process. And the three stages of the deformation process were highlighted and reasonably explicated by the number of shear transformation zones (STZs), the size of the largest STZs, and the indexes based on the Top-10 largest standard clusters. Where the shear transformation occurs closely depends on the local atomic structure of the sample, the areas of lower order and looser compaction are more prone to shear transformation, which gradually nucleated and evolved into shear bands with increased strain. Interestingly, results also revealed that the generation and propagation of shear bands conduct to the rejuvenation of the atomic structure outside the shear bands of the amorphous sample during compression. These findings improve the understanding of the generation and propagation of shear bands, so as to provide guidance for designing of new amorphous materials with desired mechanical properties.