Ecological ternary cements (ECP) were prepared with powders of phosphogypsum (PG), fly ash (FA) and Portland cement (PC). The evolution mechanism of the hydration product structure was characterized through macro and micro experiments. The thermodynamic characteristics of the solid phase, solid solution phase and aqueous solution in the process of hydration about the phosphogypsum–fly ash–cement ternary cementitious system were studied based on the Gibbs-free-energy C-S-H thermodynamic model and GEM-Selektor software and compared with the experimental results. The results show that, in the hydration reaction, the thermodynamic interaction between the mineral single-phase and hydration products plays an important role in the spatio-temporal distribution of ions in the cementitious system. The values of CaO, SiO₂^H and H₂O_hyd gradually increased with the increase in the Ca/Si ratio, while the values of CaO_ext and H₂O_OH showed a positive proportional relationship and the values of SiO₂^H and SiO₂ showed an inverse proportional relationship. GEM-Selektor accurately simulated the total amount of AFt and AFm mineral phases, and quantitatively analyzed the correlation of complex ion groups about C-S-H gels and C₃S.