Chitosan has significant advantages due to its good biocompatibility and biodegradability. However, the original chitosan often has problems such as limited adsorption capacity and poor selectivity. Therefore, modifying chitosan to improve its adsorption performance has become an important research direction. This study adopted molecular dynamics simulations to explore the factors influencing the physical modification of chitosan and further conducted adsorption experiments with three different dyes. The results indicated that when combined with different clays, the interaction between chitosan and montmorillonite was more likely to occur, making it a suitable adsorbent for physical modification. As the molecular weight (MW) of chitosan increased, the 0.99004), while lower temperature was more conducive to the adsorption process. The results would help determine the optimum synthetic conditions for chitosan-based composite materials and make positive contributions to the green development of agriculture.