Simultaneously enhancing the strength and toughness of elastomers has long been a great challenge. Inspired by the cell-like structures found in nature, this study employs phosphatidylcholine to modulate the polarity of lignin, and thereby lignin forms a self-assembly “cell-like structure” within hydroxylated polyisoprene rubber, developing a green strategy for synthesizing high-performance rubber. The mechanism underlying the self-assembly of lignin structures was elucidated through two-dimensional infrared analysis and molecular simulations. Furthermore, atomic force microscopy force-distance curve analysis revealed that the presence of phosphatidylcholine not only altered the self-assembled structure of lignin but also facilitated the formation of an interfacial layer between lignin and the rubber matrix, thereby enhancing their compatibility. The “cell-like structure” and compatibility transformation enable the formation of lignin-reinforced hydroxylated polyisoprene rubbers with outstanding mechanical properties, achieving a remarkable strength of 26 MPa and great recovery capabilities in the absence of chemical permanent crosslinking. This innovative approach pioneers a novel green pathway for the sustainable production of high-performance rubber materials.