In angiosperms, paradormancy, a phenomenon that the growth of axillary buds be arrested by the biochemical signals from other organs or tissues, has been extensively investigated in deciduous perennial woody species. However, little attention has been paid to paradormancy set and release in perennial evergreen trees. Camellia sinensis cv Huangdan develops axillary floral buds and axillary shoot buds within same leaf node simultaneously, with growing floral buds repressing shoot buds leading to their paradormancy. In this study, we manually removed the axillary floral buds, then harvested the axillary shoot buds after 1- and 3- days of the floral bud removal, untargeted metabolomics were conducted to identify metabolome remodeling patterns during paradormancy-to-growth transition. Our data suggest that the restricted supply of reducing hexose and ammonium to the axillary shoot buds could be the major cause leading to their paradormancy. The axillary shoot buds were released from paradormancy one day after the axillary floral bud removal, this transition was accompanied with mobilization and reconfiguration for multiple primary and secondary metabolites. These metabolome reprogramming could help establish the reactive oxygen species gradients along leaf bud meristem, thus facilitate paradormancy set or release. This study provides novel insights about paradormancy set and release in a perennial evergreen tree species.