To mitigate the shortage of freshwater resource in the island and coastal regions, using seawater (SW) for concrete mix can provide significant economic and environmental benefits. To achieve a safe and reliable application, in-depth investigation is needed on hydration of Portland cement in SW. The composition of solid and liquid phases in hydrated Portland cement was quantitively determined and analysed in this study. The use of SW not only significantly increases the hydration rate of clinker but also affects the evolution of phase assemblage. Both the thermodynamic calculations and experimental determinations indicates the formation of Friedel's salt (FS) instead of sulfo-AFm in hydrated cement by SW, implying sulfate ions cannot compete with chloride ions to combine with AFm phases. The characteristic reaction in SW leads to higher sulfate concentration, thus indirectly hindering ettringite (AFt) conversion at the late stage. Through the experimental quantification of thermogravimetric analysis and X-ray diffraction analysis, the kinetic model of clinker dissolution was modified to be more suitable for the hydration of Portland cement in SW. The calculation from coupled models exhibits a novel method to evaluate the evolution of phases in cement hydration. Through model calculations, 3.70% higher solid volume and 12.2% lower liquid volume were obtained in the cement-SW paste at the end of the hydration, which may cause the mechanical properties to be more sensitive under environmental humidity and the temperature.