Nanocubic pyrite (FeS₂) crystals with exposed (100) crystal faces and sizes of 100–200 nm were successfully synthesized via a facile hydrothermal method using greigite (Fe₃S₄) as the iron precursor and thiourea (NH₂CSNH₂) as the sulfur source. When the concentration of thiourea was 40 mmol/L, both pyrite and hematite were observed in the as-prepared sample, indicating incomplete conversion of greigite into pyrite. With an increased thiourea concentration to 80 mmol/L, pyrite was found to be the only crystalline phase in the synthesized samples. All greigite could be transformed to pyrite within 24 h via the hydrothermal method, while further prolonging the hydrothermal time had insignificant effect on the crystal phase composition, crystallinity, and morphologies of the prepared nanocubic pyrite crystals. In contrast, when a mixture of Na₂S and S powder was used to replace the thiourea as the sulfur source, tetragonal, orthorhombic, cubic, and irregular pyrite crystal particles with sizes of 100 nm–1 μm were found to co-exist in the prepared samples. These results demonstrate the critical influence of sulfur source on pyrite morphology. Furthermore, our hydrothermal process, using a combination of greigite and thiourea, is proved to be effective in preparing nanocubic pyrite crystals. Our findings can also provide new insight into the formation environments and pathways of nanocubic pyrite under hydrothermal conditions.