The purpose of this study was to investigate the effect of selenium nanoparticles (Se NPs) on the biomass and quality of green leafy vegetables in agriculture field. Two fields (i.e., Binhu, Wuxi and Kunshan, Suzhou) were selected to grow green leafy vegetables, namely Brassica chinensis
L. (rapeseed) and Lactuca sativa
L. var. ramosa Hort (lettuce). The results of previous experiments indicated that the optimum concentration for soil application was 0.05 mg/kg. In this study, root parameters (root length, root surface area, root volume), biomass, ascorbic acid (Vc) content, metabolite species and abundance of green leafy vegetables were analyzed. The results demonstrated that Se NPs could significantly promote root growth in green leafy vegetables. Se NPs increased the biomass of rapeseed (108.2%) and lettuce (90.9%). Specifically, the Se NPs promoted the edible parts of green leafy vegetables containing more than 0.30 mg/kg dry weight of Se. In contrast, the conventional selenium fertilizer (sodium selenite) did not promote the growth of green leafy vegetables. Additionally, Se NPs improved the photosynthesis by increasing Fe content in rapeseed (48.1%) and Mn content in lettuce (72.2%). Moreover, Se NPs increased Vc levels in rapeseed (127.5%) and lettuce (23.1%). Metabolomics analysis showed that Se NPs significantly increased the relative abundance of amino acids (22.7%) and flavonoids (37.1%) in rapeseed. Compared with sodium selenite, Se NPs not only reduced the residual amount of Se in soil, but also improved the utilization efficiency of soil nitrogen. Consequently, Se NPs can improve the biomass and quality of green leafy vegetables and reduce the potential environmental risks.