In this work, the effects of the Si/Al ratio and moisture content on thermal transport in sustainable geopolymers have been comprehensively investigated by using the molecular dynamics simulation. The thermal conductivity of geopolymer systems increases with the increase of Si/Al ratio, and the phonon vibration frequency region, which plays a major role in the main increase of its thermal conductivity, is 8−25 THz, while the rest of the frequency interval contributes less. With the increase of moisture content, the thermal conductivity of geopolymer systems decreases at first, then increases, and finally stabilizes, which is contrary to the changing trend of the porosity of the system. This is mainly because the existence of pores leads to phonon scattering during thermal transport, which, in turn, affects the thermal conductivity of the system. When the moisture content is 5%, the thermal conductivity reaches a minimum value of about 1.103 W/ (m•K), which is 40.2% lower than the thermal conductivity of the system without a water molecule. This work will help to enhance the physical level understanding of the relationship between the geopolymer structures and thermal transport properties.