Geopolymer materials have emerged as promising alternatives to ordinary Portland cementitious materials, offering more sustainable solutions for concrete production. Sodium aluminosilicate hydrate (N-A-S-H) serves as a crucial component in geopolymer concrete, while its thermomechanical properties at elevated temperatures remain relatively underexplored. This study examined the molecular structural variations of N-A-S-H within a temperature range of 300–900 K. The influence of different Si/Al ratios and temperature levels on molecular characteristics and atomic mobility was analyzed using the radial distribution function (RDF) and mean square displacement (MSD). The thermal conductivity of the N-A-S-H gel was determined using the Müller-Plathe reverse nonequilibrium molecular dynamics (RNEMD) method. Results show that as temperature increases, the mobility of Si and Al atoms is enhanced, and the thermal conductivity of N-A-S-H gel ranges from 1.431 to 1.857 W/m/K. The thermal conductivity increases with higher Si/Al ratios and elevated temperatures, suggesting decreased thermal insulation performance at higher Si/Al ratios and temperatures.