The conformational changes of hydroxyl groups affect the structure behavior directly, it is important to study the structure properties of cellulose II. In order to explore them, the molecular structure was investigated by using the molecular dynamics simulation at different temperature. The results indicate that the initial model and the force field are reasonable. With the temperature raising, the standard deviations of the glycosidic torsion angle φ of center and origin chains increase 56.56% and 38.63% respectively. Likewise, the standard deviations of torsional angle ψ of the center chains and origin chains increase 32.89% and 34.91% respectively. The increase of standard deviations of these torsional angles promote the flexibility of the hydroxyl groups and further correspond to the reduction of the hydrogen bond probability. The distance and probability of intersheet hydrogen bond O2c-Hc. . . O6c’ are the shortest and largest respectively at different temperature. This is related to only one peak of the dihedral angle τ2 in the center chain, even if the peak decreases with temperature increasing. The large fluctuation of the intrachain hydrogen bond O3-H. . . O5 in probability and distance is directly related to the glycosidic torsion angle φ rather than the dihedral angle τ3. However, the intersheet hydrogen bond O6c-Hc. . . O6o’ is very unstable and corresponds to the minimum steric hindrance for dihedral angle τ6. According to the probability, distance and angle of different hydrogen bond types, the intrasheet hydrogen bond of cellulose II crystal is more stable than that intersheet and intrachain hydrogen bonds at different temperature.