We studied crystal structure and local structure of Mg2-xPrxNi4 (x = 0.6 and 1.0) and their deuterides using in situ neutron total scattering and first-principles calculations. The total scattering data were analyzed using Rietveld refinement and pair distribution function analysis (PDF). The crystal structure of Mg2-xPrxNi4 before deuterium absorption was C15b in space group F (4) over bar 3m. No difference between the crystal and local (PDF) structures was observed. The crystal structure of Mg1.0Pr1.0Ni4D similar to 4 was found to be orthorhombic in space group Pmn2(1), with three deuterium occupation sites: PrNi3 and two types of bipyramidal Pr2MgNi2 that have a plane of symmetry composed of MgNi2. There is no significant difference between the crystal structure and the local structure of Mg10Pr1.0Ni4D similar to 4. On the other hand, the average crystal structure of the Mg-rich Mg1.4Pr0.6Ni4D similar to 3.6 was C15b with two deuterium occupation sites: PrNi3 and MgPrNi2 suggesting that the deuterium occupation shifts away from the Pr2MgNi2 bipyramid. First-principles relaxed structures also showed the shift of the hydrogen occupation site toward the Pr atom of the bipyramid, when induced by Mg substitution for the opposing Pr, resulting in hydrogen occupation in the MgPrNi2 tetrahedral site. The PDF pattern of Mg1.4Pr0.6Ni4D similar to 3.6 cannot be refined below 7.2 angstrom in atomic distances using the C15b structure which was obtained from Rietveld refinement but can be done using an orthorhombic structure. It suggests that Mg1.4Pr0.6Ni4D similar to 3.6 was locally distorted to the orthorhombic.