The hydrogen Knudsen compressor has potential applications on the hydrogen transmission for the microdevices and systems. In this paper, the numerical model of the hydrogen Knudsen compressor was established, combining the N-S continuity equations with the slip boundary conditions. The effect of structures on the performance of the hydrogen Knudsen compressor is studied by generating different obstacles in the micro channels. This paper is mainly concerned on the rectangular and the triangular obstacles, and the influence of the obstacles length and height are investigated, respectively. The Knudsen number distribution and the rarefaction of the hydrogen gas flow are analyzed. Also, the characteristic of the pressure increase for the compressor under different parameters are investigated and discussed. The effect of the structure parameters on the flow velocity distributions are detailed described, as well as the velocity contour and the vortex distributions. Moreover, the variation of the Knudsen layers of the hydrogen gas flow in the hydrogen Knudsen compressor is presented, and the key factor of the Knudsen layers is analyzed and discussed. The results is significantly beneficial for the applications and designs of hydrogen Knudsen compressor. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.