This study presents a novel three-dimensional (3D) micromechanical peridynamic (PD) model to establish relationships between microstructural features such as shape, size and distribution of fibers, damage initiation, and size-effect relationships. It specifically permits to investigate the effective elastic properties and damage mechanisms in composites. It enables the application of pure strain, pure stress and mixed stress–strain constraints while including the effect of temperature change. Also, it permits the evaluation of effective material properties from a single load case. Periodic boundary conditions are applied naturally by completing the interaction domain using material points from the opposite side of microstructure. Also, this 3D PD micromechanical model does not require any surface correction for both homogenization and dehomogenization. Complex heterogeneous microstructures of composites are constructed and analyzed by state-based PD. Material variability is taken into consideration during the progressive damage analysis to capture more realistic failure mechanisms. Peridynamic predictions recover results available in the literature; thus, verifying the accuracy and effectiveness of the present micromechanical model.