Phosphoric acid-based geopolymer (PABG) is a new amorphous cementitious material. PABG molecular dynamics (MD) simulation is carried out for the first time, using the modified Dreiding force field and the new macromolecular model. In this study, structural and mechanical properties of PABG, such as the bulk density, bond length, angle, radial distribution function (RDF), elastic modulus, and bulk modulus, are calculated by MD simulation. The bulk density is 1.85 g/cm3, close to 1.82 g/cm3 obtained in the experiment. The bond lengths of Si–O, Al–O, and P–O bonds and the angles of ∠OSiO, ∠OAlO, and ∠OPO agree well with the experimental values. The shape of the RDF curve can reflect short-range order and long-range disorder of the PABG structure. The elastic modulus is 33.42 GPa, close to 31.23 GPa measured by the nanoindentation experiment. The bulk modulus is 20.98 GPa, larger than the values obtained in the alkali-activated geopolymer (AAG) experiments. These results provide a reasonable basis for further PABG MD simulation research.