The alkali-activated metakaolin amorphous phase is mainly composed of N-A-S-H, and the alkali-activated slag amorphous phase is mainly composed of C-A-S-H. The amorphous phase components are difficult to accurately characterize by traditional methods, so it is difficult to build a real molecular model. This paper proposes a method for building a molecular model of alkali-activated gelling materials. The crystalline phase components of AAMs are obtained by Rietveld refinement and internal standard QXRD analysis. The chemical composition of the amorphous phase is analyzed by comparing with the XRF results. The short-range ordered structure of the amorphous phase of AAMs is obtained by XRD peak separation. The structures of N-A-S-H and C-A-S-H are constructed by Materials studio software, and verified by molecular dynamics simulation of radial distribution function and bulk modulus. The results show that the short-range ordered structure of N-A-S-H gel is close to that of sodalite; the short-range ordered structure of C-A-S-H gel is close to that of katoite. The accuracy of the constructed model is verified by radial distribution function and bulk modulus.