Display omitted •Polystyrene-nanoplastics (PS-NPs) enhance antioxidant activity and activate carbon metabolism.•The difference in root-related gene expressions is induced by PS-NPs.•Jasmonate and lignin biosynthesis are inhibited by PS-NPs treatments.•Exogenous JA application alleviates potential adverse effects of PS-NPs on rice seedlings. Potential adverse effects of nanoplastics (NPs) on marine organisms have received increased attention in recent years. In contrast, few data are available on terrestrial plants, especially on the mechanisms for transport of NPs in plants and phytotoxicity (at both phenotypic and molecular levels) of plants induced by NPs. To address this knowledge gap, we conducted a microcosm study in which hydroponically-cultured rice (Oryza sativa L.) seedlings were exposed to polystyrene (PS)-NPs at 0, 10, 50, and 100 mg L−1 for 16 d and examined for morphological and physiological phenotypes and transcriptomics. Laser confocal scanning micrographs confirmed PS-NPs were uptaken by rice roots, greatly benefitted from the transport activity of aquaporin in rice roots. The significant enhancement (p < 0.05) of antioxidant enzyme activities reflected the oxidative stress response of rice roots upon exposure to PS-NPs. Treatment by PS-NPs decreased root length and increased lateral root numbers. Carbon metabolism was activated (e.g., increased carbon and soluble sugar contents) whereas jasmonic acid and lignin biosynthesis were inhibited. The present study demonstrated the likelihood for transport of PS-NPs in rice roots and induced phytotoxicity by PS-NPs, which should inspire further investigations into the potential human health risks from rice consumption.