The understanding of sodium aluminosilicate hydrate (N-A-S-H) gel is still limited due to its complex and amorphous structure. Recently, molecular dynamics simulation has provided a unique opportunity to better understand the structure of N-A-S-H gel from nanoscale. In this work, the N-A-S-H gel structure was obtained by simulating the polymerization of Si and Al monomers by molecular dynamics. The simulated polymerization process is in good agreement with the experimental results especially in terms of the reaction rate of Si and Al species. The atomic structural features of the N-A-S-H gel were analyzed in terms of bond length and bond angle information, simulated X-ray diffraction (XRD) and Qn distribution. A significant finding is the existence of pentacoordinate Al in all simulated N-A-S-H structures, indicating that pentacoordinate Al in geopolymer does not only come from raw material. Besides, the results show that a smaller Si/Al ratio led to a more crosslinked and compacted structure of N-A-S-H gel.