(Pr1−zYbz)yFe4−xCoxSb12 (z = 0.25, 0.75, y = 0.8, and x = 0, 0.5, 1.0) skutterudites were prepared by using encapsulated melting, annealing, and hot pressing, and the effects of Pr/Yb partial double filling and Co charge compensation on the microstructure, charge transport and thermoelectric properties were investigated. All specimens were transformed to the skutterudite phase by using melting and annealing processes, and a few secondary phases such as marcasite FeSb2 formed together with the skutterudite phase. However, with Co substitution, the intensities of the FeSb2 peaks decreased, and proportion of the FeSb2 phase decreased with increasing Co content. Pr and Yb were confirmed to be partially double filled in the voids, and Co was substituted at Fe sites because for the Pr/Yb and Fe/Co substitution, the lattice constant changed with the filling ratio. All specimens exhibited degenerate semiconductor characteristics and p-type conduction at temperatures from 323 K to 823 K, and the charge transport properties showed a slight difference with changing filling fraction due to the difference in the valences of Pr and Yb. With increasing Pr and Co contents, the carrier concentration decreased. Consequently, the Seebeck coefficient increased, and the electrical conductivity decreased. The electronic thermal conductivity dominated the thermal conductivity, and the lattice thermal conductivity was decreased because the phonon scattering was enhanced by the Pr and Yb partial double-filling. Although the lattice thermal conductivity of partially double-filled specimens was lower than that of completely double-filled specimens, the partially double-filled specimens showed higher thermal conductivity because of the increase in electronic thermal conductivity caused by the high carrier concentration. The maximum dimensionless figure of merit, ZT = 0.85, was obtained at 723 K for (Pr0.75Yb0.25)0.8Fe3CoSb12.