Non-structural carbohydrates (NSCs) serve as key metabolic substrates and carbon reserves in plants, playing a central role in regulating vegetation carbon dynamics. Despite their importance, the global distribution and underlying drivers of NSC variations remain uncertain. We compiled a database consisting of 29,386 field measurements on NSC concentrations during the growing season, covering 1,016 sites and 2,041 species, to examine organ-specific NSC patterns and disentangle the relative contributions of environmental conditions and evolutionary history. Leaf NSC concentrations increase with latitude, whereas stem and root NSC concentrations decline, linked primarily to water availability, temperature and solar radiation. The spatial contrast reflects differentiated source–sink controls on NSC storage along environmental gradients. In contrast, NSC concentrations increase with evolutionary divergence time in leaves, but decline in stems and roots. Crucially, evolutionary history explains a larger portion (55.9–77.1%) of global NSC variations across organs, surpassing contemporary environmental controls. These findings reveal the organ-specific disparity in NSC storage and underscore the central role of evolutionary history in shaping global NSC variability, with important implications for plant carbon balance and vegetation carbon modelling.