Soil autotoxic chemosensory substances have emerged as the predominant environmental factors constraining the growth, quality, and yield of Codonopsis pilosula in recent years. Among a vast array of chemosensory substances, benzoic acid constitutes the principal chemosensory substance in the successive cultivation of C. pilosula. However, the exploration regarding the stress exerted by benzoic acid on the growth and development of C. pilosula remains indistinct, and there is a scarcity of research on the mechanism of lobetyolin synthesis in C. pilosula. In the current research, it was discovered that exposure to benzoic acid at a concentration of 200 mmol/L conspicuously attenuated the plant height, root length, total length, fresh weight, root weight, root thickness, chlorophyll content, electrolyte osmolality, leaf intercellular CO₂ concentration (C_i), net photosynthesis rate (P_n), transpiration rate (T_r), and leaf stomatal conductance (G_s) of C. pilosula. Benzoic acid (200 mmol/L) significantly enhanced the activity of root enzymes, including superoxide dismutase (SOD), malondialdehyde (MDA), and peroxidase (POD), as well as the accumulation of polysaccharides and lobetyolins (polyacetylene glycosides) in the roots of C. pilosula. In this study, 58,563 genes were assembled, and 7946 differentially expressed genes were discovered, including 4068 upregulated genes and 3878 downregulated genes. The outcomes of the histological examination demonstrated that benzoic acid stress augmented the upregulation of genes encoding key enzymes implicated in the citric acid cycle, fatty acid metabolism, as well as starch and sucrose metabolic pathways. The results of this investigation indicated that a moderate amount of benzoic acid could enhance the content of lobetyolin in C. pilosula and upregulate the expression of key coding genes within the signaling cascade to improve the resilience of C. pilosula lobetyolin against benzoic acid stress; this furnished a novel perspective for the study of C. pilosula lobetyolin as a potential substance for alleviating benzoic acid-induced stress.