Density functional theory (DFT) simulation has been recently introduced to understand the doping behavior of impurities in clinker phases. P-doped ye’elimite, a typical doping clinker phase, tends to form when phosphogypsum is used to manufacture calcium sulfoaluminate cement (CSA) clinkers. However, the substitution mechanism of P has not been uncovered yet. In this study, the influence of different doping amounts of P on the crystalline and electronic structure of ye’elimite was investigated using backscattered scanning electron microscopy–energy X-ray dispersive spectroscopy, X-ray diffraction tests, Rietveld quantitative phase analysis, and DFT simulations. Furthermore, the substitution preference of P in ye’elimite was revealed. Our results showed that increasing the doping amount of P increased the impurity contents in CSA clinkers, transforming the ye’elimite crystal system from the orthorhombic to the cubic system and decreasing the interplanar spacing of ye’elimite. Based on the calculation results of the defect formation energies, additional energies were required for P atoms to substitute Ca/Al atoms compared with those required for P atoms to substitute S atoms in both orthorhombic and cubic systems of ye’elimite. Combined calculation results of the bond length–bond order and partial density of states showed that the doped P atoms preferably substituted S atoms; the second possible substituted atoms were Al atoms, while there was only a slight possibility for substitution of Ca atoms. The substitution of P atoms for S atoms can be verified based on the elemental distribution in P-doped ye’elimite and the increasing residual CaSO4 contents. The transition of the crystal system and a decrease in the interplanar spacing for ye’elimite can also prove that the substitution of P atoms for Al atoms occurred substantially.