Fibre deformation (or shearing of yarns) can develop during the liquid moulding of composites due to injection pressures or polymerisation (cross-linking) reactions (e.g., chemical shrinkage). On that premise, this may also induce potential residual stress–strain, warpage, and design defects in the composite part. In this paper, a developed numerical framework is customised to analyse deformations and the residual stress–strain of fibre (at a micro-scale) and yarns (at a meso-scale) during a liquid composite moulding (LCM) process cycle (fill and cure stages). This is achieved by linking flow simulations (coupled filling–curing simulation) to a transient structural model using ANSYS software. This work develops advanced User-Defined Functions (UDFs) and User-Defined Scalers (UDSs) to enhance the commercial CFD code with extra models for chemorheology, cure kinetics, heat generation, and permeability. Such models will be hooked within the conservation equations in the thermo-chemo-flow model and hence reflected by the structural model. In doing so, the knowledge of permeability, polymerisation, rheology, and mechanical response can be digitally obtained for more coherent and optimised manufacturing processes of advanced composites.