Lignification causes a detrimental impact on the quality of edible sprouts. However, the mechanism of inhibition of lignification of edible sprouts by nano-selenium and lentinans remains unclear. To reveal the mechanism of lignification regulation of sprouts by nano-selenium and lentinans, this study investigated the changes in antioxidant indicators, phytohormones, polyphenols, and metabolites in the lignin biosynthesis in pea sprouts following sprays of nano-selenium or/and lentinans twice. There was an overall increase in the aforementioned indices following treatment. In particular, the combined application of 5 mg L-1 nano-selenium and 20 mg L-1 lentinans was more effective than their individual applications in enhancing peroxidase, catalase, DPPH free-radical scavenging rate, luteolin, and sinapic acid, as well as inhibiting malondialdehyde generation and lignin accumulation. Combined with the results from correlation analysis, nano-selenium and lentinans may inhibit lignification by enhancing antioxidant systems, inducing phytohormone-mediated signaling, and enriching precursor metabolites (caffeyl alcohol, sinapyl alcohol, 4-coumaryl alcohol). In terms of the results of non-targeted metabolomics, the combined application of 5 mg L-1 nano-selenium and 20 mg L-1 lentinans mainly affected biosynthesis of plant secondary metabolites, biosynthesis of phenylpropanoids, phenylpropanoid biosynthesis, arginine and proline metabolism, and linoleic acid metabolism pathways, which supported and complemented results from targeted screenings. Overall, the combined sprays of nano-selenium and lentinans showed synergistic effects in delaying lignification and optimizing the quality of pea sprouts. This study provides a novel and practicable technology for delaying lignification in the cultivation of edible sprouts. © 2023 Society of Chemical Industry.