In this paper, the numerical model of a centrifugal compressor low-flow stage is verified. The gaps and labyrinth seals were simulated in the numerical model. The task was to determine the optimal settings for high-quality modeling of the low-flow stages. The intergrid interface application issues, turbulence and roughness models are considered. The obtained numerical model settings are used to validate seven model stages for the range of the optimal conditional flow coefficient with Φopt = 0.008–0.018 and the conditional Mach number Mu = 0.785–0.804. The simulation results are compared with the experimental data. The high pressure stage-7 (HPS-7) stage with Φopt = 0.010 and Mu = 0.60 at different inlet pressure of 4, 10 and 40 atm is considered separately. Acceptable validation results are obtained with the recommended numerical model settings; the modeling uncertainty for the polytropic pressure coefficient δη*pol < 4% for the efficiency coefficient δη*pol exceeds the limit of 4% only in the two most low-flow stages, U and V.