The three-dimensional (3D) dual-energy focal stacks (FS) imaging method has been developed to quickly obtain the spatial distribution of an element of interest in a sample; it is a combination of the 3D FS imaging method and two-dimensional (2D) dual-energy contrast imaging based on scanning transmission soft X-ray microscopy (STXM). A simulation was firstly performed to verify the feasibility of the 3D elemental reconstruction method. Then, a sample of composite nanofibers, polystyrene doped with ferric acetylacetonate [Fe(acac)3], was further investigated to quickly reveal the spatial distribution of Fe(acac)3 in the sample. Furthermore, the data acquisition time was less than that for STXM nanotomography under similar resolution conditions and did not require any complicated sample preparation. The novel approach of 3D dual-energy FS imaging, which allows fast 3D elemental mapping, is expected to provide invaluable information for biomedicine and materials science.