The structural and mechanical responses of Ti-based and Zr-based metallic glasses (MGs) treated by the nanosecond laser shock wave were investigated. A rejuvenation transition was observed, due to the structural rearrangement of neighboring atoms in the instantaneous shock process. Plenty of embryonic shear bands occurred along the shock-affected zone. A damped model of the shock pressure was established to describe the characteristic of the embryonic shear bands. The results showed that the shear band initiation in the nanosecond scale along the length direction was divided into two stages: the initial low propagation stage and the following fast propagation stage, because of the reduction of the shock pressure. The hardness of the shock-affected zone displayed a maximal decrease of 25% in the critical zone between the two propagation stages, due to the combined effect of the structural rejuvenation and the compressive residual stress. A schematic of the energy landscape was proposed to explain the relationship between the rejuvenation and the formation of the embryonic shear bands. The maximum tensile plasticity increased by 0.46%. The results demonstrated that the MGs possessed different shear band propagation modes in the initiation stages, which deepened the understanding of the deformation mechanism in the MGs.