The pyrochlore supergroup minerals (PSM) are typical secondary phases that replace (with zirconolite–laachite) earlier Sc-Nb-rich baddeleyite under the influence of F-bearing hydrothermal solutions, and form individual well-shaped crystals in surrounding carbonatites. Like primary Sc-Nb-rich baddeleyite, the PSM are concentrated in the axial carbonate-rich zone of the phoscorite-carbonatite complex, so their content, grain size and chemical diversity increase from the pipe margins to axis. There are 12 members of the PSM in the phoscorite-carbonatite complex. Fluorine- and oxygen-dominant phases are spread in host silicate rocks and marginal carbonate-poor phoscorite, while hydroxide-dominant PSM occur mainly in the axial carbonate-rich zone of the ore-pipe. Ti-rich PSM (up to oxycalciobetafite) occur in host silicate rocks and calcite carbonatite veins, and Ta-rich phases (up to microlites) are spread in intermediate and axial magnetite-rich phoscorite. In marginal (apatite)-forsterite phoscorite, there are only Ca-dominant PSM, and the rest of the rocks include Ca-, Na- and vacancy-dominant phases. The crystal structures of oxycalciopyrochlore and hydroxynatropyrochlore were refined in the (Formula Presented) space group with R₁ values of 0.032 and 0.054 respectively. The total difference in scattering parameters of B sites are in agreement with substitution scheme ^BTi⁴⁺ + γOH^- = ^BNb⁵⁺ + γO^2-. The perspective process flow diagram for rare-metal “anomalous ore” processing includes sulfur-acidic cleaning of baddeleyite concentrate from PSM and zirconolite–laachite impurities followed by deep metal recovery from baddeleyite concentrate and Nb-Ta-Zr-U-Th-rich sulfatic product from its cleaning.