The pressure dependence of the crystal structure of a powder sample of HgBa2CaCu2O6.3 (Tc=123 K) was studied in the pressure range of 0 to 3.6 GPa, using the DN-12 time-of-flight diffractometer at the IBR-2 pulsed reactor and a sapphire anvil cell chamber. At P=0 the results are in a good accordance with the published data. At P=3.0 and 3.6 GPa the best fit of the experimental data was achieved using the structural model with apical oxygen disordered in the (a,b) plane. The compressibility values of the lattice constants and selected bonds were calculated from the structural data. The highest absolute value of compressibility was found for the distance between the Ba and O atom layers.