Continuous misuse of difenoconazole (DFZ) results in farmland contamination, posing risks to crops and human health. Salicylic acid (SA) has been shown to enhance plant resistance and reduce pesticide phytotoxicity and accumulation. However, whether SA effectively reduces DFZ phytotoxicity and accumulation and its underlying mechanisms remain poorly understood. To address this, a short-term indoor experiment and a long-term outdoor pot experiment were conducted to evaluate the potential of SA to alleviate DFZ-induced phytotoxicity and its effects on DFZ uptake, translocation, metabolism, and accumulation. The underlying mechanisms were explored through physiological, biochemical, and gene expression analyses. The results showed that DFZ induced oxidative damage and reduced photosynthesis by 15.6% in wheat. SA upregulated the expression of genes encoding antioxidant enzymes (POD, CAT, SOD1, and SOD2) in the roots and leaves of DFZ-exposed plants, leading to a 7.5%-13.4% increase in antioxidant enzyme activities and a subsequent 9.7%-14.5% decrease in reactive oxygen species levels. Additionally, SA increased the total chlorophyll content by 16.3%, which was enhanced by regulating chlorophyll synthesis and degradation-related genes, thereby improving the net photosynthetic rate by 12.2%. Furthermore, SA upregulated the expression of lignin biosynthesis-related, CYP450, and GST genes, which reduced DFZ uptake and accelerated its degradation. Consequently, the wheat grain DFZ content decreased by 36.2%, thus reducing the health risk index. This study confirms the potential of SA to reduce DFZ phytotoxicity and accumulation. Based on these findings, we recommend using SA in DFZ-contaminated areas to mitigate phytotoxicity and the associated human dietary exposure risks.