The Shazi deposit is a newly discovered, potential large-scale scandium deposit located in Qinglong, southwestern Guizhou Province, China. The iron isotopic composition of magnetite in fresh basalt, weathered basalt, and mineralized laterite was investigated. The Fe content of fresh basalt and of weathered basalt vary from 15.41 wt.% to 15.51 wt.% and from 14.60 wt.% to 15.12 wt.%, respectively, while the δ56Fe of magnetite varies from 0.23‰ to 0.29‰ and from 0.02‰ to 0.07‰. Laterite has the highest Fe content, in the range of 23.53%~28.95%, but δ56Fe is similar to weathered basalt, and the range of variation is −0.09‰–0.03‰. The change in iron isotope composition in weathered basalt and laterite is related to the hydrolysis of clinopyroxene. Combined with the existing research results, the genesis of scandium deposit is considered to be related to in situ hydrolysis in deep and surface weathering leaching of Emeishan basalt.