The effect of oxidation on the structure and properties of polyesters remains an urgent issue due to the prospects for regulating the stability of the polymer and modifying its surface. The available data on the effect of ozone on the structure and properties of poly-3-hydroxybutyrate (PHB), in particular on the rate of its destruction, are contradictory. So, the purpose of the work was to study the effect of ozone oxidation on structure and properties of PHB to find the impact of the ozone treatment on controlling the rate of the biodegradation in environmental conditions. The surface of PHB films was modified using ozone treatment to accelerate its biodegradation rate in soil. The essence of ozonation is in the accumulation of various oxygen-containing functional groups, which leads to increased intermolecular interaction of PHB chains, which leads to the hardening of the surface. It was shown that the ozone treatment of the surface slowed down the diffusion of destructors to the volume of the PHB and prevented the fragmentation of the film. In addition, the strength of the films after 5 h of ozonation increased from 25 to 42 MPa, but the wetting angle did not change and no significant change in the surface crystallinity were detected before the soil exposure of the films. The soil burial test showed an approximately 1.5-fold decrease in the biodegradation rate for the ozone-treated sample. This study demonstrated that the surface morphology created by ozone treatment formed a unique outer layer of a new morphology. Ozonated PHB films were more resistant to fragmentation and remained stable in the soil for 300 days, while the control sample of PHB completely decomposed in 240 days. The paper discusses the causes and consequences of these observations and the role of ozone treatment for the modification of PHB surface. The results obtained can be used to control the rate of degradation and to predict the behavior of sterilized products in the field of packaging, medical products, and products with a limited service life due to the understanding of mechanism of surface modification.