Rapid development of multiscale modelling techniques has enabled significant improvement in understanding material failure. However, accurate simulation of general anisotropic materials still remains a great challenge. This is due to the unbalanced number of material parameters required by models of different scales, and it is difficult and sometime impossible to extract micro material properties from known macro properties. This paper proposes a new 3D discrete element model (DEM) to take full interactions between material particles for general anisotropic composite materials. The challenging issue in determining the micro bond properties of the 3 DEM model is resolved by coupling machine learning (ML) technique with the genetic algorithm (GA). The learned bond properties are validated by comparing DEM predicted macro material properties with experimental results. The micro bond properties are further used to predict strength and simulate crack patterns of bolted composite lap joints. The predictions of the ML model agree well with experimental results of the joints.