We studied in situ the local atomic structure evolution of an equiatomic ${\mathrm{Zr}}_{50}{\mathrm{Cu}}_{50}$ metallic glassy alloy under high pressure compression inside a diamond anvil cell using synchrotron x-ray total scattering. The empirical potential structure refinement method was used to reconstruct the three-dimensional atomic models at each pressure step, and to analyze the spatially averaged local atomic structure configurations. The interatomic distances of different atomic pairs are reduced at different rates with increasing pressure and the Cu-Cu pairs exhibit the highest percentage reduction. Between ambient pressure and 36.85 GPa, the atomic separation of the Cu-Cu pairs is reduced by ∼12% compared to ∼5% for Zr-Zr and Zr-Cu pairs. Such disproportional decrease in interatomic distance results in inhomogeneous atom reconfiguration in the short atomic range. With the increase of pressure, the Zr atoms move preferentially towards the Zr-Zr pairs, while the Cu atoms move preferentially towards the Cu-Cu pairs, creating inhomogeneous atom reconfiguration with positive short-range order coefficients of 0.0309 and 0.0464 for Zr-Zr and Cu-Cu respectively, but a negative value of −0.0464 for Zr-Cu pairs. Voronoi tessellation method was also used to study the evolution of the short-range atom packing versus pressure, elucidating the cause for the bimodal distribution of the bond angle distributions. The research sheds light on understanding of the atomic reconfiguration of equiatomic alloys under high pressure.