The development of tree peony annual shoots is characterized by “withering”, which is related to whether there are bud points in the leaf axillaries of annual shoots. However, the mechanism of “withering” in tree peony is still unclear. In this study, Paeonia ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’ were used to investigate dynamic changes of annual shoots through anatomy, physiology, transcriptome, and metabolome. The results demonstrated that the developmental dynamics of annual shoots of the two cultivars were comparable. The withering degree of P. suffruticosa ‘Luoyanghong’ was higher than that of P. ostii ‘Fengdan’, and their upper internodes of annual flowering shoots had a lower degree of lignin deposition, cellulose, C/N ratio, showing no obvious sclerenchyma, than the bottom ones and the whole internodes of vegetative shoot, which resulted in the “withering” of upper internodes. A total of 36 phytohormone metabolites were detected, of which 33 and 31 were detected in P. ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’, respectively. In addition, 302 and 240 differentially expressed genes related to lignin biosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, and zeatin biosynthesis were screened from the two cultivars. Furtherly, 36 structural genes and 40 transcription factors associated with the development of annual shoots were highly co-expressed, and eight hub genes involved in this developmental process were identified. Consequently, this study explained the developmental dynamic on the varied annual shoots through multi-omics, providing a theoretical foundation for germplasm innovation and the mechanized harvesting of tree peony annual shoots.