When transporting natural gas over long distances, it is necessary to build gas compressor stations that compensate for the gas energy losses due to friction. The uninterrupted supply of natural gas to consumers depends on their reliability. Current trends in increasing power with a simultaneous decrease structure stiffness leads to the occurrence of previously unpredictable oscillations of the compressor rotor. The article describes the main causes of compressor rotor vibrations and some methods of dealing with them. Due to the limitations of the considered phenomena with this methods, the article proposes the use multiphysics modeling of gas and structure interaction using the 2FSI approach. Simulation performed for a simplified labyrinthseal compressor rotor model. To solve the problem, the ANSYS software product was chosen, which implements the 2FSI method. The calculations were carried out on a high-performance computing complex PNRPU. For the model structure, an analysis of natural frequencies is performed and a Campbell diagram is constructed. The trajectories analysis of a point on shaft rotation axis at different rotation frequencies of the rotor is carried out. The influence of the imbalance on the dynamics of the system is noted. Further, the results of numerical modeling of the structure taking into account gas dynamics are presented and the results comparison by dynamic modeling of the structure is carried out. To identify the factors influencing the rotor dynamics, taking into account gas dynamics, numerical calculations were carried out with various options for taking into account the effect of gravity and imbalance.