This paper is devoted to three-dimensional simulation of gas flows in in microchannels of complex technical systems. For simulation the multiscale approach combining the solution of quasigasdynamic equations and the molecular dynamics within the method of splitting into physical processes is used. Parallel implementation is based on the domain decomposition method and the functional parallelism and is oriented on use of computing systems with the central and hybrid architectures. In paper the calculations of three-dimensional nitrogen, hydrogen and their mixtures flows are made, comparing of the received results with the experimental data is carried out. Analysis of the obtained results confirms the efficiency of the offered approach and shows the good scalability of the developed parallel code.