3D FE (finite element) simulations of the deformation and damage evolution of particle reinforced composites are carried out for different microstructures of the composites. Several new methods and programs for the automatic reconstruction of 3D microstructures of composites on the basis of the geometrical description of microstructures as well as on the basis of the voxel array data have been developed and tested. Different methods of reconstruction and generation of finite element models of 3D microstructures of composite materials (geometry-based and voxel array based) are discussed and compared. It was shown that FE analyses of the elasto-plastic deformation and damage of composite materials using the microstructural models of materials generated with these methods yield very close results. Numerical testing of composites with random, regular, clustered and gradient arrangements of spherical particles is carried out. The fraction of failed particles and the tensile stress-strain curves were determined numerically for each of the microstructures. It was found that the rate of damage growth as well as the critical applied strain, at which the damage growth in particles begins, depend on the particle arrangement, and increase in the following order: gradient < random < regular < clustered microstructure.