In order to reveal the physiological response of sunflower to broomrape parasitism and its related metabolic pathways, the resistant-broomrape sunflower material (s41) and the sensitive-broomrape sunflower material (s26) were used as the test materials to inoculate the broomrape. Transcriptome sequencing analysis of 4 samples under the condition of parasitic stress in broomrape was carried out, and physiological verification analysis of some key substances was carried out. The results showed that the number of DEGs was 6362, 6609, 5490 and 5469 by screening the differential genes among the samples. GO analysis showed that the s26-s41, s26CK-s41CK, s26-s26CK, and s41-s41CK 4 comparison groups had more differential genes involved in biological processes, followed by cellular components, and less involved in molecular functions; KEGG analysis showed that Infection has a great influence on plant signal transduction, biosynthesis of secondary metabolites, lipid metabolism, amino acid metabolism and sugar metabolism in sunflower. The measurement results of physiological indicators showed that the enzymes involved in phenylpropane metabolism, antioxidant substances, and salicylic acid all showed an upward trend, indicating that under the parasitism of broomrape, the anti-stress system was activated, but the physiological indicators related to sense and anti-materials changed. The difference is that the gene expression that controls the relevant physiological indicators is different. The results laid the foundation for revealing the molecular mechanism of resistance broomrape.