The wide application of nano-particles (NPs) has raised a serious concern over their impact on plants. However, evaluation of the effects of NPs on plant metabolism by direct detection of chemicals inside solid tissues presents a challenge. In this study, we report on a direct ionization method in mass spectrometry, internal extractive electrospray ionization (iEESI), for the direct evaluation of phytotoxicity of three different NPs (including CdTe quantum dots (CdTe QDs), gold nano-particles (Au NPs), and silver nano-particles (Ag NPs)) both on surfaces and inside solid tissues from the mung bean seeds (Vigna radiata) that were cultured in aqueous solutions of three NPs at 50 μg mL-1. The results showed that NPs could stimulate the biological accumulation of trigonelline and the decomposition of polysaccharides/oligosaccharides to glucose and maltose within 21 h of culture. To the best of our knowledge, this is the first study to apply internal extractive electrospray ionization mass spectrometry (iEESI-MS) for the direct measurement of solid tissue samples to evaluate the phytotoxicity of NPs on mung bean sprouts. Our study lays a solid foundation for further examination of other NPs-induced damaging effects such as apoptosis/necrosis, helping us to understand the phytotoxicity of NPs on plants.