One of the key parameters characterizing the microstructure of a layer is its degree of order. It can be determined from optical studies or X-ray diffraction. However, both of these methods applied to the same layer may give different results because, for example, aggregates may contribute to the amorphous background in XRD studies, while in optical studies, they may already show order. Because we are usually interested in the optical and/or electrical properties of the layers, which in turn are closely related to their dielectric properties, determining the optical order of the layers is particularly important. In this work, the microstructure, optical properties and electrical conductivity of poly(3-hexyl)thiophene layers were investigated, and a model describing the electrical conductivity of these layers was proposed. The model is based on the generalized theory of the effective medium and uses the equation from the percolation theory of electrical conductivity for the effective medium of a mixture of two materials. The results indicate a key role of the aggregate size and limited conductivity of charge carriers, mainly due to structural imperfections that manifest themselves as an increase in the number of localized states visible in the subgap absorption near the optical absorption edge. The critical value of the order parameter and the corresponding values of the Urbach energy, excitonic linewidth and band gap energy are determined.