Nowadays, the development and research of nonwoven medical fibrous materials based on biopolymers is an area of a great practical interest. One of the most promising methods for producing nonwoven materials with a highly developed surface is electrospinning (ES). In this article, the possibility of efficient sterilization of ultrathin fibers based on polyhydroxybutyrate (PHB) by ozone treatment was considered. The purpose of this work was to select the most optimal morphology of nonwoven materials for medical purposes and to establish the correlation between the supramolecular structure and the physical properties of fibrous materials while under the influence of an ozone sterilization process.