Currently, one of the most common microdefects are cracks in the transversal layers of composite materials. There is also a decrease in the elastic modulus and shear modulus of composite materials during cracking of transversal layers. One of the most dangerous places of fatigue damage in structures are stress concentrators: joints, areas of holes for hatches in the wing. In this paper, the accumulation of damage in the area of the junction of the wing console with the center section of the aircraft is investigated, taking into account fatigue durability. An algorithm for calculating the accumulation of damage on the example of this zone is proposed. In the course of the work, a micromechanical approach is used, which is the most effective for describing the accumulation of damage. Previously, the optimization problem is solved by determining the rational zone of the junction node. After determining the rational length of the joint zone, a butt joint is designed. Then the stress-strain state of the structure is determined. Next, the zones and types of cracks are determined. The calculations assumed that cracking occurs in the transverse direction between fibers. In the crack zone, the damaged layer is unloaded, and the adjacent layers, therefore, are reloaded. As a result of this study, an algorithm was obtained that takes into account the influence of the current stress state on the process of degradation of mechanical properties. An analytical calculation was also carried out on the example of the junction of the wing console with the center section of the aircraft. Changes in the elastic modulus and shear modulus for the composite structure are obtained depending on the number of cycles. The dependence of stiffness in the composite structure taking into account the length of the interlayer crack is also shown. The algorithm obtained in this work is planned to be used to predict changes in various structures of composite materials depending on damage under the action of cyclic loading.