The environmental migration and bioavailability of Hexavalent chromium (Cr(VI)) could be affected by facet-dependent pyrite (FeS2) existing in soils and sediments. Conversely, the occurrence state of facet-dependent FeS2 might also be influenced by Cr(VI). However, the complex interactive mechanism at the solid–liquid interface between facet-dependent FeS2 and Cr(VI) still remained ambiguous. Herein, FeS2 nanobelts, FeS2 nanosheets, and FeS2 nanocubes with corresponding dominant facets of (−110), (001), (100)/(210) were prepared. The adsorption and reduction experimental results reflected that Cr(VI) species were predominantly adsorbed and a portion of them was reduced to Cr(III) at the FeS2 interfaces. In particular, the adsorption efficiency of Cr(VI) on (001) facet was 1.39 and 4.69 times than those on (−110) and (100)+(210) facets, respectively. The results of in situ Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) measurements and Density Functional Theory (DFT) calculations suggested that bidentate binuclear (BB) coordinated chromates were generated on the (001) facet while monodentate mononuclear (MM) coordinated chromates were formed on (−110), (100), and (210) facets. Due to the stronger adsorption energy and more stable coordination mode of BB for Cr(VI) species on (001) facet, FeS2 NS exhibited higher efficiency of Cr(VI) removal and reduction compared with FeS2 NB and FeS2 NC. In addition, partial FeS2 particles were proved to be transformed to goethite under the effect of Cr(VI). Owing to the stronger adsorption of Cr(VI) species on (001) facet, FeS2 NS also had a faster phase transformation rate than FeS2 NB and FeS2 NC. Above results all reflected the good structure–reactivity relationships between the FeS2 facets and the Cr(VI) removal efficiency as well as the phase transformation of FeS2 particles.