Sulfur-source dependent pyrrhotite nanoparticles (Fe1-XS (X 0–0.2)) were synthesized using ferric chloride and four different water-soluble sulfur sources, sodium thiosulphate, sodium sulfide, thiourea, and thioacetamide (referred to as IS-1, IS-2, IS-3, and IS-4, respectively), via a wet mechanochemical route without an inert atmosphere. Owing to the different dispersing sulfur environments and different bond energies of sulfur from different sources, pyrrhotite NPs with different shapes, sizes, band gap, and sulfur contents were obtained and that affects their catalytic activities. XPS of sulfur showed that the sulfide/polysulfide ratios of IS-1, IS-2, IS-3, and IS-4 were determined to be 3.48, 2.67, 1.29, and 1.94, respectively. Several classes of organic dyes, such as rhodamine B-RhB, methyl orange-MO, methylene blue-MB, Nile blue-NB, crystal violet-CV, and their mixtures, were used to explore the sonocatalytic dye degradation of the synthesized natural pyrrhotite NPs. The dye degradation efficiency was in the following sequence: IS-1 (highly active and reactive, 100% removal efficiency in 1 min) >> IS-2 (selective for RhB and MB) > IS-4 (moderately active) > IS-3 (inactive). The generation efficiency of reactive oxygen species using the pyrrhotite NPs under the sonocatalyic process was the same sequences of the sulfide/polysulfide ratio, which were the key factor affecting the sonocatalytic activity and stability during dyes degradation. Iron with different valence states allow faster electron transfer reaction and the presence of S2−/Sn2− redox couples improved the stability of the catalyst. Furthermore, the catalyst was reusable with similar reactivity and removal efficacy, even after five catalytic cycles.