Understanding the doping behaviors of impurity ions in mineralogical compositions is of great significance for optimizing the quality of sulphoaluminate cement (SAC) clinker as well as its performance in engineering utilizations. The key issue is determining the exact existing state of these impurity ions. Here, combined with experiments and density functional theoretical (DFT) simulations, we systematically studied the substitution preference of chromium in the three main composed phases of SAC clinker, i. e, C 4 A 3 S̅, C 2 S and C 4 AF. The formation energies indicate that Cr ions prefer to enter C 4 AF by substituting Fe ions followed by incorporating into C 4 A 3 S̅ with replacement of S ions. The results from X-ray diffractions of single phase show the successful incorporations of Cr ions into both individual mineral, C 4 AF and C 4 A 3 S̅. The dominant content of C 4 A 3 S̅ in SAC clinker is well illustrated from Rietveld refinement. Further proof of the doping preference is from the difference in relative amounts of Cr(III) and Cr(VI) in SAC clinker samples with lower dosages. More in-depth analyses from both electron contributions and bond order-bond length distributions show that the substitution preference follows the "electronic structure matching" principle, which ensures the effective substitution by forming stronger bonds between guest ions and oxygen atoms. The doping preference provides a possibility of controlling the valence state of Cr ions by tuning the mineralogical compositions of SAC clinker, thus is essential in guiding the synthesis of SAC-based materials by utilizing Cr-bearing solid waste. [Display omitted] • The substitution preference of Cr ions in SAC clinker phases is studied by experiments and DFT simulations. • Cr ions prefer to incorporate into the composed mineral C 4 AF by substituting Fe ions. • Cr ions can also enter into the dominant mineral C 4 A 3 S̅ by substituting S ions. • The preference can be attributed to similar electron contributions between Cr and Fe ions. [ABSTRACT FROM AUTHOR]