Single-crystal synchrotron X-ray diffraction, Raman spectroscopy, and first principles calculations have been used to identify the structure of the high-pressure (HP) phase of molecular methane above 20 GPa up to 71 GPa. The structure of HP phase is trigonal R3, which can be represented as a distortion of the cubic phase B, previously documented at 7-15 GPa and confirmed here. The positions of hydrogen atoms in HP phase have been obtained from first principles calculations. The molecules occupy four different crystallographic sites in phases B and eleven sites in the HP phase, which result in splitting of molecular stretching modes detected in Raman spectroscopy and assigned here based on a good agreement with the Raman spectra calculated from the first principles. Our study points out to a single HP phase unlike up to three HP phases proposed previously based on the Raman spectroscopy results only.