The widespread presence and potential harm conferred by polycyclic aromatic hydrocarbons (PAHs) to various organisms have raised increased research interest on these pollutants. Plants lack of efficient PAH degradation genes so that they had to suffer from PAH stress. To improve the ability of plants to tolerate various PAHs, four genes, namely nidA and nidB (encoding the large and small subunits of naphthalene dioxygenase of Mycobacterium vanbaalenii PYR-1) as well as nahAa and nahAb (encoding flavoprotein reductase and ferredoxin of the electron-transport chain of the Pseudomonas putida G7 naphthalene dioxygenase system), were ectopically expressed in rice. The hybrid multicomponent naphthalene dioxygenase can assemble correctly and break down PAHs powerfully. Transgenic rice plants exhibited enhanced tolerance toward two- to four-ring PAHs. PAH tolerance in transgenic plants was associated with high chlorophyll levels and photosynthesis efficiency, normal development, and minimal ion leakage under PAH stress. The naphthalene metabolic pathway in transgenic plants mainly involves the dioxygenase pathway. Our results indicate that grafting the naphthalene dioxygenase system into plants is useful to degrade PAHs efficiently in vivo and improve the plant tolerance to the pollutants. This study had introduced a suitable strategy to accelerate the bioremediation process of PAH-contaminated soil under waterlogged conditions and improve the food safety in contaminated area.