Slag, an important supplementary cementitious material, is widely utilized for producing sustainable cement-based materials. In this paper, to study the effect of hydration stage and composition on the microstructure of cement-slag powder composites, the hydrated tricalcium silicate (CS) curing at 20 °C at 28-day and 90-day with slag dosage from 0% to 45% were investigated by Si and Al NMR spectrum and molecular dynamics. Silicate connectivity from Si NMR test showed that with increasing slag substitution content, the mean chain length (MCL) of the CS-slag hydrated paste at 28-day increased from 2.99 to 4.02 and the AlO/SiO ratio rose from 0 to 0.043. Aluminate coordinates of Al NMR analysis revealed that the incorporation of slag could contribute to transformation from ettringite to Aft and formation of Al [4] in the C-A-S-H gel. Furthermore, reactive force field molecular dynamics was utilized to study the structural, reactivity and mechanical properties of C-A-S-H gel in hydrated composite. The AlO species in the C-A-S-H gel played an essential role in healing the defective silicate chains and transforming dimmer-rich silicate chains at low slag powder content to a long aluminate-silicate skeleton with high slag powder content. The structural evolution was attributed to the polymerization reaction between aluminate species and non-bridging silicate tetrahedron, with neighboring water molecule dissociations. In respect of dynamical properties, the aluminate-silicate structure exhibited good stability due to high Al–O–Si connection characterized by time correlated function. Uniaxial tensile modeling revealed that C-A-S-H gel with long aluminate-silicate chains exhibits good loading resistance and the cohesive strength of C-A-S-H gel is improved to a great extent due to the incorporation of slag powder. Hopefully, this study may provide molecular insights for design of sustainable and durable cement-slag powder composites.