Microplastics (MPs) can influence the availability of contaminants in the soil and have adverse effects on plants. Up to now, the effects of MPs on the uptake of organic pollutants by leguminous plants are still unclear. In this study, we explored the impacts and mechanisms of polystyrene MPs of different sizes on the uptake of phenanthrene (Phe) by soybean seedlings. The results showed that MPs decreased the uptake of Phe in soybean roots and leaves. Micron-size MPs showed a higher inhibition of Phe uptake in roots than nano-size MPs (4.83 mg/kg) at the beginning with concentrations of 1.89 mg/kg, 3.40 mg/kg, and 0.72 mg/kg in groups 1 mum, 10 mum, and 100 mum MPs/Phe, respectively. The combined toxicity of micron-size MPs and Phe to soybean plants was higher than that of nano-size MPs and Phe, and 100 mum MPs and Phe co-contaminant show the highest toxicity to soybean. The activities of antioxidative enzymes and their gene expression showed that micron-size MPs induced higher genotoxic and oxidative damage to soybean roots than nano-size MPs, which decreased the activity of roots, thus leading to the lower uptake of Phe by soybean roots and leaves. This study highlights that the combined exposure to MPs and Phe causes harmful effects on soybean plants and MPs inhibit the uptake of organic pollutants by higher plants.