Abstract: Chemical composition design of raw materials is the basis of hydration reaction and mechanical strength formation of excess-sulfate phosphorgypsum slag cement (PPSC). Laboratory experiments and molecular dynamics simulation (MD) provide a multi-scale regulation and control design basis for chemical composition of PPSC raw materials. The structural model of the PPSC was established by Materials Studio (MS). The effect of the molar ratios of chemical components on the compressive strength of PPSC was studied by means of MD simulation and XRD. The results show that with the increase of the CaO/SO₃ molar ratio and the decrease of SiO₂/Al₂O₃, the compressive strength of PPSC shows an increasing trend. When the SiO₂/Al₂O₃ molar ratio is 3.5-3.7 and the CaO/SO₃ molar ratio is 1.8~2.0, the compressive strength of PPSC is higher. The MD simulation result of PPSC pore structure is contrary to the compressive strength test result, which proves the reliability of the simulation result. At the atomic scale, MD simulation shows that O, Ca, Al and S atoms exhibit high diffusion ability. In the alkaline environment, sulphate activation increases the bond length of S=O, Al—O and O=O, and the structure is unstable and hydrolyzed, resulting in more ettringite that promotes strength. By adjusting the raw materials SiO₂/Al₂O₃ molar ratio and CaO/SO₃ molar ratio, PPSC can form a more stable internal structure. The design of chemical composition molar ratio and MD simulation methods are of great significance for the composition design and application promotion of PPSC.