Jujube powder is prone to moisture absorption, caking, and sticking during spray drying and storage, significantly affecting product quality and shelf-life stability. Its stability is closely related to the glass transition behavior of the amorphous sugar system. To reveal the molecular mechanism of the structural instability of the non-crystalline carbohydrate matrix induced by water, and to provide a theoretical reference for understanding the moisture absorption stability of high-sugar food systems such as jujube powder, using the amorphous glucose as the model system, the effects of different water contents on the glass transition and microscopic structure of the system were studied by molecular dynamics methods. Based on the COMPASS Ⅲ force field, the model was constructed, and the volume-temperature curve was obtained by gradually cooling to determine the glass transition temperature. Combined with the mean-square displacement and radial distribution function, the regulatory effects of water on molecular diffusion and hydrogen bond networks were analyzed. The results showed that as the water content increased from 0% to 20%, the Tg decreased from 335.05 K to 290.75 K; when the water content increased from 5% to 10%, the Tg decreased from 331.44 K to 311.62 K, a decrease of 19.82 K, and the system changed from a glassy state to a rubbery state. The diffusion analysis indicates that at 320 K, as the water content increases, the slope of the MSD curve of glucose molecules gradually increases. The self-diffusion coefficient increases from 1.75×10-11 m2·s-1 in the low water content state to 1.54×10-10 m2·s-1 in the high water content state, increasing by approximately 8.8 times. The microstructure analysis shows that water molecules preferentially form hydrogen bonds with the hydroxyl groups of glucose. The first peak of RDF is located at approximately 2.8 Å. This changes the interaction mode between sugar molecules and promotes the reconstruction of the hydrogen bond network, thereby increasing the free volume of the system, promoting molecular migration, and ultimately leading to a decrease in the glass transition temperature and a reduction in structural stability. The research results can provide a theoretical basis for the stability regulation of sugar amorphous systems and the control of moisture absorption during the storage process after spray drying of jujube powder, as well as the optimization of packaging and the regulation of quality stability.