In this study, green composites were prepared using natural rubber (NR) as the matrix and the sisal microcrystalline cellulose (MCC) as the filler. Three modifying agents oleic acid (OA), γ-aminopropyltriethoxylsilane (KH550), and bis-γ-(triethoxysilylpropyl)-tetrasulfide (Si69) were individually tested to modify the MCC to improve the interfacial compatibility of the NR and MCC. Combined with modern instrumental analysis technology and molecular dynamics simulation, the reinforcing effect and microscopic mechanism of modified MCC on NR were analyzed. The structure-activity relationship of NR and MCC composites was further revealed, and the interaction between the two components was clarified. At the same time, the reinforcing and compatibilizing effect of three kinds of modified MCC in NR matrix were also revealed. The results showed that the properties of NR/Mod-MCC composites were better than those of NR/MCC composites, where NR/OA-MCC presented the highest tensile strength, followed by NR/Si69-MCC. In addition, NR/Si69-MCC exhibited higher elongation at break and NR/KH550-MCC exhibited higher vulcanization characteristics. Molecular model systems were constructed through molecular dynamics simulation to investigate the interactions between the three modified cellulose molecules and the NR molecules.OA-cellulose has a better interaction with NR than KH550-cellulose and Si69-cellulose, The simulation results were consistent with the experimental results.