A progressive damage model is proposed to investigate the damage initiation and evolution of 3D woven composites under uniaxial compression at a micromechanical level. The typical compressive experiments were carried out. Based on the observations, the compression failure modes of 3D woven composites mainly include fiber kinking, transverse failure of fiber tow, matrix fracture, and interfacial debonding. The initial damage criteria are according to the physically based failure criteria for the fiber kinking, the Puck criteria for the transverse failure of fiber tow, and the maximum stress criterion for the matrix. The damage of fiber tow–matrix interfacial is simulated through cohesive contact. Particularly, the fiber’s initial misalignment angle is taken into account in the damage model. The simulated compression results agree well with the experimental ones. The compressive stress–strain response of the 3D woven composite is forecasted. The damage evolution of each constituent of the 3D woven composite is obtained. The results show that the influence of the fiber’s initial misalignment angle on the compression strength of the 3D woven composite needs to be considered.