An amorphous/crystalline metallic composite (A/C-MC) integrates metallic glass with crystalline metals in one system. The amorphous-crystalline interface (ACI) in A/C-MCs under deformation absorbs dislocations and may fundamentally change the dilemma that the strength comes at the expense of the ductility of a material. However, the development of such materials is still at a trial and error stage due to the lack of a clear-cut understanding on how the amorphous component become instable when a dislocation-mediated plasticity flows into the glassy phases. To meet this need, here we focus on gaining the physical insights into the dislocation-ACI reaction in A/C-MCs through atomistic simulations. We have (i) digitally resembled an interface structure close to that in experiments by annealing melted metallic glasses at cooling rates as low as  ∼ 104 K/s; (ii) correlated the dislocation absorption events with the activation of shear transformation zones (STZs) in A/C-MCs under a plastic shear; (iii) identified the mechanisms responsible for a continuous dislocation absorption-induced instability in glassy phases; (iv) calibrated a set of constitutive relations, kinetic rules, and model parameters that can be used in an effective temperature concept-based STZ theories at the continuum level; and (v) characterized the local stress states ahead of the instability band and lay the macroscopic-level glass instability criterion on a firm atomistic basis. Our major findings are: (a) there exists a nanoscale structure transition at the ACI when the cooling rate in the atomistic simulations is reduced to an experimentally-comparable level; (b) the number of atoms participating in the STZs exponentially increases with the number of dislocations arriving at the ACI at an early stage of the dislocation-ACI reaction, but is linearly proportional to the number of absorbed dislocations at a later stage; (c) the dislocation absorption-induced instability in metallic glasses occurs through a three-stage process, i.e., the activation of STZs in the region between icosahedral (ICO) clusters, the coalescence of newly formed STZs, and then the breakdown of ICOs; (d) the model parameters in the continuum-level constitutive relations and kinetic rules are found to be sensitive to cooling rates; and (e) the local stress states ahead of the instability band in glassy phases map surprisingly well with the Mohr-Coulomb criterion regardless of the applied stress at the macroscopic level. The gained knowledge may provide a pathway of connecting the atomistic deformation physics of an A/C-MC with its overall mechanical performance, which is currently difficult to achieve in laboratory experiments.