Recently, the trend of replacing cement with mineral admixtures in concrete has witnessed increasing interest in the construction industry due to the reduction in embodied energy and CO2 emissions. However, the addition of these admixtures in Portland Cement (PC) affected the formation as well as the structure of the hydration product Calcium-Silicate-Hydrate (C-S-H), which is reflected in the mechanical and durability properties of cement concrete. In the present study, nano-silica (NS) and a mixture of fly ash (FA) and NS were replaced into PC (PC + 0.5 % NS, PC + 1 % NS, PC + 0.5 % NS + 20 % FA and PC + 1 % NS + 40 % FA) to systematically study the formation and structural evolution of hydration products, namely C-S-H, at atomic and micro-scales at the early stage of hydration (3 days) and a later stage of hydration (90 days). The formation and structure of C-S-H were analyzed to correlate the microstructure development by using XRD, Rietveld technique, FESEM, TEM, FTIR and nano-scale mechanical properties by employing the nanoindentation techniques. Atomic Pair Distribution Function (PDF) is used to understand the effect of admixtures on the C-S-H structure from atomic point of view. PDF shows the structural modification of C-S-H such as different polyhedral, separation of intralayer/interlayer, pair/bond length, coordination number of atoms corresponding to the addition of additives with hydration age. Also, porosity measurements show increasing or decreasing porosity during hydration with additives. It is observed that the contribution of low-density C-S-H (LD C-S-H) is greater than that of high-density C-S-H (HD C-S-H) in the beginning days, whereas HD C-S-H more than LD C-S-H in the latter days of hydration. The elastic modulus increased from 15.44 GPa to 19.82 GPa and the hardness decreased from 0.41 GPa to 0.35 GPa of LD C-S-H in early days, whereas elastic modulus decreased from 34.84 GPa to 29.33 GPa and the hardness increased from 0.75 GPa to 0.83 GPa of HD C-S-H in the latter stage due to addition of additives. However, both increased for LD C-S-H and HD C-S-H for each corresponding mixture during hydration. The present study reported the formation and microstructural modifications of C-S-H and the correlation with nano-mechanical properties due to addition of nano or micro-sized admixtures (nano silica and fly ash) in the cement system. This correlation helps to develop low-energy cement composites by tailoring cement systems with desired properties.