The initial changes in the microstructure of alkali-activated slag cement (AAS) characterize the rheological behavior, initial structuration, and setting times of the mixture. In this study, the relationships among the rheological behavior, solidification process, and nanostructure changes of sodium hydroxide-activated slag (NH–AAS) and sodium silicate-activated slag (SS–AAS) pastes over time are investigated by small amplitude oscillation shear test, isothermal calorimetry, scanning electron microscopy analyses, and 1H–29Si cross-polarization magic-angle spinning nuclear magnetic resonance spectroscopy (CP MAS NMR) and 29Si MAS NMR spectroscopy. Test results showed that the NH–AAS reaches its initial setting time following a continuously proceeding structuration process, whereas the SS–AAS reaches its initial setting with an abrupt increase in the structuration process. At their initial setting times, the NH–AAS and SS–AAS mixtures release similar heat and reach a similar reaction degree. The SS–AAS mixture had more N–A–S–H formation than C–A–S–H at the initial setting time. On the other hand, the amount of C–A–S–H was similar to N–A–S–H in the NH–AAS mixture. The gradual N–A–S–H gel degradation to form C–A–S–H was observed during the acceleration period for the SS–AAS mixture.