The role of root‐derived dissolved inorganic carbon (DIC) has been emphasized lately, as it can provide an alternative source of carbon for photosynthesis. The fate of newly fixed DIC and its effect on non‐structural carbohydrate (NSC) pools has not been thoroughly elucidated to date. To this end, we used ¹³C (NaHCO₃) as a substrate tracer to investigate the incorporation of newly fixed bicarbonate into the plant organs and NSC compounds of Camptotheca acuminata seedlings for 24 and 72 h. NSC levels across the organs were all markedly increased within 24 h of labeling treatment and afterward only decreased in stems at 72 h. The variation range of NSC concentrations in roots was considerably smaller than in the stem and leaves. As time passed, the δ¹³C in NSC compounds was significantly affected by ¹³C labeling and was more positive in the roots than in the stem and leaves. Starch was more ¹³C‐enriched than was soluble carbohydrate, and the δ¹³C of root starch was as high as −4.70‰. Bicarbonate incorporation into newly formed NSC compounds contributed up to 0.24% of the root starch within 72 h. These data provided strong evidence that bicarbonate not only acted as a C source that contributed slightly to the NSC pools but also stimulated the increase in NSC pools. The present study expands our understanding of the rapid change of NSC pools across the organs in response to bicarbonate.