The model of the filled polymer is considered. This model takes into account the following factors: the aggregation of particles of the filler; the interfacial layer. The numerical method of calculating the effective heat conductivity of composite systems is offered. The method consists in the direct solution of the heat conductivity equation. We resolve the heat conductivity equation with the use of the finite-difference scheme. The method offered allows to do calculations for various distributions of the filler in a matrix. Besides, we can consider the influence of an interfacial layer on thermal properties of a composite. The comparison of the calculated and experimental data is done.