In order to study the effect of different modification methods on polysilsesquioxane (POSS) modified cellulose, a molecular dynamics method was used to establish a pure cellulose model and a series of modified models modified by polysilsesquioxane in different ways. And their thermodynamic properties were calculated. The results showed that the performance of cellulose models was better than that of unmodified model, and the modified effect was the best when two cellulose chains were grafted onto polysilsesquioxane by chemical bond (M2 model). Compared with pure cellulose model, the cohesive energy density and solubility parameters of M2 model are increased by 9%, and the values of tensile modulus, bulk modulus, shear modulus and Cauchy pressure increased by 38.6%, 29.5%, 41.1% and 29.5%, respectively. In addition, the free volume fraction and mean square displacement of each model were calculated and analyzed in this work. Compared with the pure cellulose model, the molecular chain entanglement of cellulose was increased due to the existence of the chemical bonds in the M2 model, which made the cellulose molecular chains occupy more free volume, so that the system had a smaller free volume fraction, inhibited the chain movement of cellulose chains, and thus improved the thermal stability of cellulose.