This study explores the encapsulation dynamics and interaction mechanisms of catechin derivatives within single-walled carbon nanotubes (SWNTs) using molecular dynamics simulations. We assessed the strength of π-π stacking interactions between catechin derivatives and SWNTs by analyzing the distance evolution between aromatic rings, mean square displacement (MSD), and diffusion coefficient (D) values. The results revealed that interaction strength varied depending on the specific derivative and concentration. At low and medium concentrations, weaker interactions were observed for catechin, epicatechin, and epigallocatechin, while stronger interactions were found for epicatechin gallate and epigallocatechin gallate. Furthermore, MSD values indicated normal diffusion trends for catechin, epicatechin, and epigallocatechin, suggesting free movement within SWNTs. In contrast, sub-diffusion trends were observed for epicatechin gallate and epigallocatechin gallate, indicating limited mobility. This study offers insights into the interactions of catechin derivatives with SWNTs, enriching our understanding of supermolecular structure development and enabling potential applications in drug delivery, and biosensors.