The doping mechanism of Ba in sulfoaluminate cement (SAC) clinker was systematically studied. Results from density functional theoretical simulations, backscattered electron diffraction and X-ray diffraction show that Ba ions prefer to incorporate into the mineral C 4 A 3 S ¯ by substituting Ca atoms while little enter into the other two minerals, C 2 S and C 4 AF. Such doping preference was also certified by the results of individual mineral of C 4 A 3 S ¯ and C 4 AF, respectively. Further analyses from partial density of states, electron density difference and local distortions indicate that the Ba-doping preference in C 4 A 3 S ¯ is attributed to the efficiency of newly formed bonds, which is enhanced by electronic structure matching and small local distortions. The understandings are essential in guiding the production of Ba-bearing SAC clinker by utilizing industrial barium slags, thus should be very important in sustainable production of SAC clinkers, environmental governance and industrial collaborative disposal of waste. [Display omitted] • Ba ions prefer to incorporate into the mineral C 4 A 3 S̅ by substituting Ca atoms. • Almost no Ba ions enter into the other two minerals of C 2 S and C 4 AF. • The small local distortion between Ca–O/Ba–O determines the preference in C 4 A 3 S̅. • It provides a possibility of producing sulfoaluminate cement with Ba-bearing waste. [ABSTRACT FROM AUTHOR]