New and enhanced functions were potentially imparted to the plant organelles after interaction with nanoparticles. In this study, we found that ~ 44% and ~ 29% of the accumulated graphene in the rice leaves passively transported to the chloroplasts and thylakoid, respectively, significantly enhanced the fluorescence intensity of chloroplasts, and promoted about 2.4 times higher adenosine triphosphate production than that of controls. The enhancement of graphene on the photophosphorylation was ascribed to two reasons: One is that graphene facilitates the electron transfer process of photosystem II in thylakoid, and the other is that graphene protects the photosystem II against photo-bleaching by acting as a scavenger of reactive oxygen species. Overall, our work here confirmed that graphene translocating in the thylakoid promoted the photosynthetic activity of chloroplast in vivo and in vitro, providing new opportunities for designing biomimetic materials to enhance the solar energy conversion systems, especially for repairing or increasing the photosynthesis activity of the plants grown under stress environment.