The coal industry plays an essential role in China’s economic development, and issues such as occupational health and environmental pollution caused by coal dust have attracted a great deal of attention. In accordance with the principles of environmental protection and waste management, this study used carboxymethyl ginkgo cellulose (CL) extracted and modified from Ginkgo biloba leaves as a matrix, and a graft copolymerized with sodium 3-allyloxy-1-hydroxy-1-propanesulfonate (AHPS) and N-isopropylacrylamide (NIPAM) monomers to prepare low-cost, environmentally friendly, and high-performance coal dust suppression (C-A-N). By optimizing fitting experimental data through three factors and two response surface analyses, the optimal dust suppression efficiency ratio was determined to be 4:8:5, and its swelling and water retention properties were analyzed. The microstructure, chemical reaction process, combustion performance and crusting property of the dust suppression gel were analyzed using Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetry (TG), scanning electron microscopy (SEM), cone calorimetry, and consolidation layer strength tests. Relevant experiments show that the dust suppression gel prepared in this study has the characteristics of a strong wettability and minor impacts on the calorific value of coal, as well as green and environmental protection. When the wind speed is 10 m/s, the dust suppression effect reaches 93%, and the hardness of the solidified layer reaches 39.6 KPa. This study analyzed the migration and combination of functional groups in the interaction system using molecular dynamics simulation software. The microscopic effect and mechanism between dust suppression gel and coal are revealed from a molecular point of view. The feasibility and accuracy of the molecular dynamics simulation were verified by the consistency between simulation results and experimental data. Therefore, combining the utilization of waste resources with dust suppression can have important economic and social benefits.