Computer simulation is a method resorted to more and more frequently for the development of the prospective power supply systems, in particular the vessel power supply system. It provides valuable insights into the transient processes and indicators of electric power quality in the system without building its physical model, thus significantly improving the efficiency and quality of the physical model. Nowadays MathLab package with Simulink application is used with increasing frequency for simulation of such systems. The paper presents a model of the power supply system of small hydrographic vessel ‘Vaygach’ built in MatLab environment. The system vulnerabilities and their remedies have been identified. Changes in sinusoid before and after the non-linear load on the network have been demonstrated and solutions for improving the non-linear distortion factor are proposed. The model developed for the vessel power supply system can be used for building models of different vessels.