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<i>Paraphoma chrysanthemicola</i>, an endophytic fungus isolated from the roots of <i>Codonopsis pilosula</i>, influences salicylic acid (SA) levels. The interaction mechanism between SA and <i>P. chrysanthemicola</i> within <i>C. pilosula</i> remains elusive. To elucidate this, an experiment was conducted with four treatments: sterile water (CK), <i>P. chrysanthemicola</i> (FG), SA, and a combination of <i>P. chrysanthemicola</i> with salicylic acid (FG+SA). Results indicated that <i>P. chrysanthemicola</i> enhanced plant growth and counteracted the growth inhibition caused by exogenous SA. Physiological analysis showed that <i>P. chrysanthemicola</i> reduced carbohydrate content and enzymatic activity in <i>C. pilosula</i> without affecting total chlorophyll concentration and attenuated the increase in these parameters induced by exogenous SA. Secondary metabolite profiling showed a decrease in soluble proteins and lobetyolin levels in the FG group, whereas SA treatment led to an increase. Both <i>P. chrysanthemicola</i> and SA treatments decreased antioxidase-like activity. Notably, the FG group exhibited higher nitric oxide (NO) levels, and the SA group exhibited higher hydrogen peroxide (H₂O₂) levels in the stems. This study elucidated the intricate context of the symbiotic dynamics between the plant species <i>P. chrysanthemicola</i> and <i>C. pilosula</i>, where an antagonistic interaction involving salicylic acid was prominently observed. This antagonism was observed in the equilibrium between carbohydrate metabolism and secondary metabolism. This equilibrium had the potential to engage reactive oxygen species (ROS) and nitric oxide (NO).