The adverse effects of emerging pollutant microplastics on plants have been fully explored, but there is limited information on how to alleviate these impacts. Here, we investigated the effects of co-exposure with polyvinyl chloride microplastics and zinc oxide nanoparticles (PVC + nZnO) in soil on yield and nutritional quality of purple waxy corn grains at 10, 20, and 30 days after pollination. Results showed that PVC + nZnO increased fresh ear weight and improved grain nutritional quality, particularly by promoting the accumulation of protein, starch, sucrose, alanine, glutamate, and aspartate. A flavonoids-targeted metabolomics detected 185 flavonoid metabolites, with a significant increase in total flavonoids content under PVC + nZnO. Key flavonoid constituents identified included astragalin, nicotiflorin, quercimeritrin, dihydrokaempferol, eriodictyol, isorhamnetin, kaempferol, and naringenin chalcone. Dynamic transcriptomicis revealed that these nutrients accumulation was regulated at transcriptional level. Additionally, WGCNA identified 54 hub genes, which could be utilized as potential targets for improving nutritional quality of waxy corn.