Increased requirements for new models of equipment in various fields of mechanical engineering lead to the need to use modern structural materials, which by their characteristics should exceed traditional materials. The use of polymer composite materials (PCM) in the creation of structural elements has become widespread. With all the advantages, PCM products are sensitive to internal defects that can appear at various stages of production and operation. The paper describes General principles of modeling layered structures with consideration for internal defects between layers using software systems (LS-DYNA, Siemens Femap) based on the finite element method (FEM) using an explicit scheme for integrating a complete system of FEM equations. The results of calculations for layered thin-walled structures made of a high-modulus polymer composite and subjected to non-stationary loads are presented, namely: a rectangular plate and a smooth flat cylindrical panel under the influence of a pressure field, a reinforced flat cylindrical panel and a smooth cylindrical shell under the action of an explosive spherical wave. The behavior of the above-mentioned layered structures with and without elliptical defects is analyzed. The fields of stress, strain, and displacement in the mono-layers at various times are determined. Safety factors coefficients are calculated using the following criteria: Hashin, Chang-Chang, Puck, LaRC03, Fischer. The degree of influence of interlayer defects is estimated. The developed method allows us to consider the influence on the strength of interlayer defects of any shape, size and location between the layers of the composite package (CP).