To understand the relation of the glass-forming ability (GFA) to the atomic configurations of Pd42.5Ni7.5Cu30P20 (PNCP) metallic glass having the best GFA at present, the local structures were investigated by combining data obtained anomalous x-ray scattering, x-ray and neutron diffraction and applying reverse Monte Carlo modeling. By comparing the results of PNCP with Pd40Ni40P20 and Pd40Cu40P20 having a slightly and much worse GFAs, respectively, characteristic features were observed in the hyper-ordered atomic structures around the secondary metals of Ni and Cu, such as the concentration inhomogeneity, the fraction of pure and slightly distorted icosahedra, and the existence of large persistent homology rings. The structural heterogeneity for the excellent GFA of PNCP would be considered by an incompatible mixture of covalent-like Pd-P configurations and icosahedral clusters around the secondary metals.