Jujube witches’ broom disease is a significant threat to jujube trees.To reveal the key biological pathways associated with disease resistance in jujube germplasm in response to phytoplasma infection， a graft-inoculation method was used to evaluate the resistance of 324 jujube germplasm resources to this disease.The study utilized disease-resistant germplasms ‘QS10’，‘UU12’，‘EQ15’ and the susceptible germplasms ‘Zhongyangmuzao’，‘Hupingzao’，‘Luzhao 5’ as materials.The phytoplasma content in leaf tissues was measured at 90 days and 120 days post-infection，and transcriptome sequencing was conducted to elucidate the differential responses.The results showed that the concentration of phytoplasma in resistant germplasm was low and gradually decreased after grafting，while the concentration of phytoplasma in susceptible germplasm was higher and gradually increased over time.The DEGs of both resistant and susceptible germplasm were significantly enriched in pathways such as plant-pathogen interaction，plant hormone signal transduction，and biosynthesis of secondary metabolites.Notable differences were observed in the expression of genes related to peroxisome，photosynthetic pathway and flavonoid biosynthesis pathway.WGCNA analysis revealed that core genes such as lipid phosphatase，RNA editing factor MORF 3，LysM domain receptor-like kinase，and serine/threonine protein kinase sty13-like were associated with resistant germplasm.Research indicated that in response to phytoplasma invasion，the differential expression of genes involved in plant-pathogen interaction，synthesis of secondary metabolites，plant hormone signal transduction，and MAPK signaling pathways may contribute to the differential phenotypes observed between resistant and susceptible germplasms.The peroxisome-related genes are upregulated in disease-resistant germplasm，while photosynthetic genes are less affected by phytoplasma invasion，which may contribute to the normal progression of energy metabolism and redox balance of resistant germplasm，thereby enhancing its disease resistance.Additionally，secondary metabolites such as flavonoids and terpenes may play a role in eliminating the damage caused by active oxygen.