As a crucial management strategy for crop diseases, pests and weeds, the use of pesticides can also have some adverse effects on plant health. Understanding the specific mechanisms is essential for developing effective mitigation measure. However, most studies on phytotoxicity mechanism have focused on ionic balance and biochemical responses, with little consideration given to pesticide distributions within plants. Herein, symptoms and the underlying mechanisms of fosthiazate phytotoxicity to crops represented by tomatoes were investigated. Necrotic leaf edge and the root inhibition of tomato seedlings was observed after fosthiazate soil applied at the maximum registered dose. Given its high hydrophilicity, fosthiazate dissolved in soil solution was readily absorbed by plant roots and efficiently translocated upward via the transpiration stream, leading to varying concentrations across different organs and thus differential phytotoxicity. As fosthiazate accumulates, it induced plasmolysis, triggered reactive oxygen species (ROS) bursts, and disrupted photosynthesis, resulting in leaf wilting and necrotic. The interference of sucrose synthesis, transport and metabolism further inhibited root growth. Fosthiazate-loaded microcapsules could alleviate its phytotoxicity by slowing down the release rate. Our findings provided an important basis for the improvement of pesticide application safety and guiding the development of chemicals targets at specific organisms.