Abstract: To investigate the effects of pesticide application on plant metabolism and growth, in this study UPLC-QTOF-MS non-targeted metabolomics technology was used to detect and evaluate the differences in root exudates of tomato (Solanum lycopersicum) treated with clothianidin at the modes of root application and foliar application, and the effects of clothianidin applied at the two different modes on the growth of tomato plants grown in soil. The results showed that the application of clothianidin significantly changed the abundance and composition of tomato root exudates, with a significant difference between the two application modes. Specifically, compared with the control, both root and foliar application of clothianidin significantly changed the β diversity of tomato root exudates, but the effect of root application was more significant; clothianidin application significantly reduced the α diversity of tomato root exudates, and the decrease was greater with the foliar application than with the root application; in addition, compared with the control, root application showed a significant increase in the abundance of 37.63% of metabolites, a significant decrease in the abundance of 12.58% of metabolites, including an increase in the abundance of biological alkaloids related to plant defense systems and inhibition of the synthesis of lipids, organic acids and other metabolites; foliar application showed a significant increase in the abundance of 35.16% of metabolites, a significant decrease in the abundance of 13.42% of metabolites, including an increase in the abundance of biological alkaloids, but inhibition of the synthesis of phenolic acids, and an opposite trend in the abundance of sulfate and stearic acid under different application modes. Additionally, both root and foliar application of clothianidin significantly promoted the growth of tomato plants, resulting in increased fresh weight, plant height, and root length compared to the control group. However, there was no significant difference in the impact on plant growth between the two application modes. This study can provide a reference for assessing the ecological risk of pesticides and guiding the efficient and rational use of pesticides.