The perennial genetically modified Populus 741, exhibiting sustained overexpression of PtoCYCD3;3, consistently shows adaxial curvature and pronounced surface wrinkling. To investigate these morphological changes, TMT quantitative proteomics and phosphoproteomics were performed on leaves of transgenic and wild-type plants. Quantitative proteomics identified significant changes in protein abundance associated with photosynthesis, phytohormones, and cell proliferation. Notably, histone deacetylase 6 (HDA6), ANGUSTIFOLIA (AN), and cellulose synthase-like (CSL) proteins associated with leaf curling were significantly upregulated in transgenic poplar. Phosphoproteomics revealed enrichment of proteins such as HERK1, DGK, OST1, and BIG, which are involved in brassinosteroid (BR), abscisic acid (ABA), and other phytohormone signaling pathways. These analyses demonstrated the impact of exogenous gene PtoCYCD3;3 integration on photosynthetic pathways, hormone signaling, and cell proliferation, highlighting its role in modulating leaf morphogenesis in perennial Populus 741.