The development of a methodology for modeling the wear surface of deadwood bearings based on optical scanning is considered in the paper. It is noted that the deadwood bearings of the ship’s shaft line wear out unevenly during operation, which affects the stress-strain state of the shaft and the system parameters responsible for the occurrence of resonance of transverse, torsional and longitudinal vibrations. The methodology and results of an experimental study of bearing wear surfaces are presented. The applied optical scanning scheme makes it possible to obtain high-precision digital models of objects due to synchronous shooting of an object with two cameras. The measurement results are obtained by processing with specialized software. The results obtained are an addition to the methodology for determining the elastic force acting on the shaft from the side of a bearing that is unevenly worn along the length with a non-constant gap. Based on the obtained wear values, a solid-state model is constructed and the natural frequencies of transverse, torsional and longitudinal vibrations are determined. For the constructed model, the forms of natural oscillations for practically significant frequencies are obtained. It is noted that bearing wear affects not only the displacement of the natural frequencies values, but also the oscillations shape. The impact of the wear of the aft bearing on the bearing capacity of the shaft line, taking into account the contact interaction, is evaluated. The simulation has shown that the bearing wear surface forms an area of increased contact pressures that arise from the impact of the propeller shaft. Analysis of the propeller shaft tip has revealed the presence of an area of increased concentration of equivalent stresses formed at the place of bearing wear formation. The proposed method of modeling the deadwood bearings wear allows us to evaluate its effect on the magnitude of the displacement of natural frequencies and the change in the bearing capacity of the shaft line. The results obtained in this work are an addition to the existing calculations in the design and evaluation of the ship’s power plant reliability.