With the continuous development of modern science, the application of computer technology helps to explain the complex physical and chemical phenomena in the field of biomass researches. Molecular dynamics simulation has been implemented for the morphology and binding mode, the chemical conversion mechanism, and the new materials formation way of biomass component (cellulose, hemicellulose and lignin). In this work, a method combining experiment and molecular dynamics simulation was developed to study the solvent effect and chemical conversion mechanism of biomass-based small sugar molecules. The calculation results, including radial distribution function, spatial distribution function and hydrogen bond distribution, demonstrated that the affinity between solvent and solutes (reactant and product) would influence the reaction process. The molecular dynamics simulation also showed the distribution of catalyst, for instance, sodium lignosulfonate concentrated around the C3 and C4 hydroxyl group of glucose, and aluminum ions were first attracted by the C2 hydroxyl group of the cellulobiose monomer, which provides a new way for analyzing the hydrolysis mechanism. The understanding of the solvent effect and chemical conversion mechanism can be employed to optimize the rate and selectivity for production of biomass-based renewable fuels and chemicals, which may provide a new insight for exploring the biorefinery process.