Different poplar varieties vary in their tolerance to certain pathogens. However, knowledge about molecular regulation and critical responses of resistant poplars during pathogen infection remains scarce. To investigate adaptive responses to canker disease caused by the bacterium Lonsdalea populi, we screened three poplar varieties with contrasting tolerance, including Populus deltoides. ‘Zhonglin 2025’ (2025), Populus × Euramericana. ‘74/76’ (107) and Populus tomentosa cv ‘henan’ (P. tomentosa). Transcriptomic analysis revealed significant changes in the expression levels of defence‐related genes in different poplar varieties in response to infection, which reshaped the PTI and ETI processes. Intriguingly, photosynthesis‐related genes were found to be highly expressed in the resistant variety, whereas the opposite was observed in the susceptible variety. Susceptible poplars maintained the activation of defence‐related genes during early period of onset, which restricted the expression of photosynthesis‐related and auxin signal‐related genes. Furthermore, combined with metabolomic analysis, differences in the content of antibacterial substances and key differentially expressed genes in phenylpropane and flavonoid biosynthesis pathways were identified. Delayed induction of catechin in the susceptible variety and it's in vitro antibacterial activity were considered to be one of the important reasons for the differences in resistance to L. populi compared with the resistant variety, which is of practical interest for tree breeding. Moreover, the trade‐off between growth and defence observed among the three poplar varieties during infection provides new insights into the multilevel regulatory circuits in tree‐pathogen interactions.

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