ABSTRACT Atractylodes lancea (Thunb.) DC . is a traditional Chinese medicine in China with extensive clinical applications and a high market demand. There is a significant quality difference between A. chinensis (Bunge) Koidz . and A. japonica Koidz. ex Kitam ., which seriously impacts its clinical efficacy. Atractylodin is determined by high‐performance liquid chromatography (HPLC). Transcriptomics combined with metabonomics is employed to elucidate the component differences between A. chinensis (Bunge) Koidz . and A. japonica Koidz. ex Kitam . It is found that ACC, PAL, and NOS are the key genes related to the synthesis of Atractylodes lancea (Thunb.) DC . According to the metabolomics data, the decreased content of salicylic acid in A. chinensis (Bunge) Koidz . may lead to a reduction in its ability to mediate the elicitor of endophytic fungi, resulting in the downregulation of the expression of the TGAL4 transcription factor and the upregulation of the DOGL3 transcription factor in A. chinensis (Bunge) Koidz . cells, which may affect the accumulation of Atractylodin. The above study provides a theoretical basis for elucidating the biosynthesis pathway of Atractylodin differences between A. chinensis (Bunge) Koidz . and A. japonica Koidz. ex Kitam .