The work for the first time highlights the specific nanoparticulate form of hexamolybdenum cluster complexes [{Mo6I8}(L)6]2− with L = CF3COO− and C6F5COO− (Mo6) exhibiting high anticancer potential in the irradiation-free conditions. The diverse nanoparticulate forms developed from the Mo6-units include self-aggregated (Bu4N)2[{Mo6I8}(L)6 (Mo6-aggregates) and those deposited onto the specifically decorated silica nanoparticles (SNs). The chemical and colloid stabilities of the as prepared nanoparticles reveal both Mo6-aggregates and those deposited onto the preliminary hydrophilized by polyethyleneimine (PEI) SNs (Mo6-PEI-SNs) as optimal candidates for biomedical applications. High photodynamic activities of Mo6-aggregates and Mo6-PEI-SNs revealed by the spin trap facilitated ESR technique along with the efficient irradiation-induced cytotoxic effects of both nanoparticulate forms indicate their great potential in photodynamic therapy. However, “dark” cytotoxicity measurements for M−HeLa cancer and Chang Liver normal cell lines revealed significant specific anticancer effect of Mo6-aggregates, but the insignificant one of Mo6-PEI-SNs. Quantitative LysoTracker-facilitated colocalization analysis in lysosomal compartments highlighted the highest lysosomal localization of Mo6-aggregates for L = CF3COO−, to a lesser degree for L = C6F5COO−, for Mo6-PEI-SNs being the lowest. The great anticancer effect of the Mo6-aggregates correlates with their highest localization in lysosomal compartment followed by the enhanced aggregation, in turn, derived from the hydrophobic apical ligands.