Heterogeneous-structured laminates (HSLs), which consist of multiple layers of metallic materials arranged in successive pairs of coarse-grained (CG) and nano-grained (NG) layers, have been recently reported to display excellent balance of strength and ductility. However, it is argued that accompanying state-of-art numerical models developed to simulate the deformation of this specific class of composite materials have limitations for investigating their underlying damage evolution. Addressing this issue is essential to support the rational design, optimisation and application of HSLs, especially when subjected to contact and dynamic processes. For this reason, a novel 3D numerical framework for HSLs is proposed and tested in this research considering published experimental findings and dislocation theories. This framework comprehensively considers the evolution of various types of dislocations and back stress while being coupled with the Johnson Cook damage criterion. The HSL specimens simulated here were made of alternating layers of CG and NG copper separated by interface affected zones. Following initial microhardness and uniaxial tensile simulations on homogenous copper with different grain sizes, simulations of HSLs were conducted to study the effect of different layer thickness and the volume fraction of the NG layer. Overall, a good correlation between numerical and experimental results was achieved. An important and distinguishing characteristic of this research is that the proposed model enables the evolution of internal damage and the synergetic effect between the CG and NG layers to be investigated. Through the evaluation of the damage accumulation factor in the NG layer, the simulations results yielded quantitative information which aligned with the following known experimental observations: 1) the smaller the layer thickness, then the smaller the internal damage and 2) the internal damage increases with the increase in volume content of the NG layer. In addition, for a set simulated strain of 10%, the developed model could be used to show that the damage accumulation factor in the NG layer was 10 times lower than that in its counterpart, i.e., a stand-alone NG layer not sandwiched between two CG layers.