Coral aragonite exhibits extreme mechanical anisotropy with elastic moduli varying by factor of two and yield strengths by 30% across crystallographic directions[1,2]. Understanding this behaviour is critical for predicting coral skeleton failure under ocean acidification. We present a computational framework in MOOSE (Multiphysics Object Oriented Simulation Environment)[3] bridging molecular dynamics to finite element analysis of coral microstructures. The framework implements a smooth quadric yield surface[4] with orthotropic elasticity calibrated from aragonite properties (E1=140.4 GPa, E2=70.3 GPa, E3=63.0 GPa) and direction-dependent yield stresses (4100-5340 MPa). The model features five post-yield modes including exponential softening, validated against all six independent loading directions. A robust two-stage return mapping algorithm ensures stability during material softening characteristic of brittle coral failure. Our approach integrates cohesive zone models (CZM) for protein-water interfaces between crystals. MD simulations reveal interfaces are 6-30 times weaker than bulk aragonite (σ ~ 180-700 MPa vs 4100-5340 MPa)[2]. The exponential CZM captures smooth traction-separation behaviour[5], enabling prediction of intergranular versus transgranular fracture in hierarchical structures. Representative Volume Element simulations of sclerodermite microstructures (10-100 µm) contain multiple grains with realistic orientations. Parametric studies show organic interface content dramatically affects response: 5-15% interfacial area reduces bulk strength by more than an order of magnitude versus perfect bonding. Loading direction sensitivity emerges from crystal texture, with misaligned boundaries containing interfaces as preferential failure sites. The validated framework enables quantitative prediction of coral mechanical properties from microstructure, providing a tool for assessing climate change impacts on reef ecosystems. This approach is transferable to other hierarchical materials including bone, nacre, and technical ceramics where interface engineering determines performance.