Nano-silica (NS) is one of the most commonly used nanomaterials in alkali-activated materials (AAMs). Differing from other inactive nanoparticles, as an active Si source, the pozzolanic activity of NS has a significant effect on the hydration reaction and properties of alkali-activated materials. In this study, activated Si in the activator was replaced by NS to prepare alkali-activated slag/fly ash cementitious materials. The effects of different dispersion methods (dry-mix (MD), water dispersion (WD), and activator dispersion (AD)) of NS on the fluidity, rheological properties, and setting time of fresh pastes were investigated. Effects of NS and reactive Si in the activator on the hydration process of alkali-activated slag/fly ash paste were investigated using isothermal calorimetry and the Krstulović-Dabić hydration model. ICP-OES was utilized to study the changing behavior of the composition of the fresh paste pore solution during the hydration reaction. The results show that ions in the pore solution change continuously with the hydration time and eventually stabilize. The stabilized pore solution is mainly composed of OH- and Na+. Different NS dispersion methods have significant effects on paste workability, rheology, and setting time. Activator dispersion can elevate the content of active Si in the activator, causing changes in the hydration process of the paste, especially for the initial hydration period. NS has the most significant effect on the hydration process due to its pozzolanic activity compared to nucleation and filling effects. The Krstulovic-Dabic model can roughly simulate the hydration kinetics possessed of alkali-activated NS/slag/fly ash after entering the accelerated period.