Abstract: Endophytes and host plants establish a mutualistic relationship. Understanding plant–endophyte–pesticide interactions is critical to revealing the functional roles and application potential of endophytes. In this study, rice was selected as a model plant and thiamethoxam as a representative pesticide to explore the interaction effects among plants, endophytes, and pesticides. Under thiamethoxam stress at concentrations of 0, 1, and 10 mg/L, normal seedlings carrying endophytes exhibited reductions in reactive oxygen species (ROS) content by 21.12%, 17.09%, and 8.19%, and in malondialdehyde (MDA) content by 22.13%, 21.33%, and 6.05%, respectively, compared with aseptic seedlings. These findings indicate that endophytes effectively mitigate oxidative damage and lipid peroxidation in rice seedlings. Concurrently, under the same thiamethoxam stress, the chlorophyll content (SPAD value) and root activity of normal seedlings were higher than those of aseptic seedlings. These parameters increased by 8.00%-25.00% and 3.29- to 4.65-fold, respectively, suggesting endophyte colonization enhances improved photosynthetic capacity and root vigor under pesticide stress. Regarding pesticide residue distribution, no significant difference in thiamethoxam content was observed between normal and aseptic seedlings at 1 mg/L thiamethoxam treatment, either in whole plants or shoots. However, at 10 mg/L thiamethoxam treatment, thiamethoxam content in normal seedlings was significantly higher than that in aseptic seedlings. Notably, root concentrations in normal seedlings were 1.80- to 5.22-fold higher than those in shoots, implying that endophytes promoted pesticide uptake and facilitated translocation to aerial tissues. Conversely, the aseptic seedlings accumulated more thiamethoxam in roots than normal seedlings, likely due to disruption of the root barrier and increased permeability. Reinoculation of endophytes significantly reduced ROS and MDA levels in aseptic seedlings, further confirming their protective role. Overall, endophytes enhanced rice tolerance to pesticide stress by synergistically regulating the antioxidant defense system, maintaining photosynthesis, and sustaining root vigor. These findings provide theoretical support for utilizing endophytic bacteria to bolster crop stress resistance and promote green agricultural development.