An autofluorescent inclusion (AFI) specifically accumulated in mesophyll cells (MCs) of non-salt-secretor mangrove was found to be related to salt, but its biosynthesis and spatial distribution characteristics remain unclear. Here, Kandelia obovata served as the experimental material, and the composition of AFI was identified as condensed tannin (CT). Na contents increased in purified AFIs under NaCl treatment, while Na+ efflux in MCs was lower than the control. In vitro, Na+ addition caused aggregations of AFIs. Proteins related to Na+/H+ and vesicle transport were identified in the purified AFIs by liquid chromatography-mass spectrometry. TEM images revealed the structures involved in CT biosynthesis in chloroplasts and CT accretions in vacuoles were more visible under higher salinity. Spatial metabolomics analysis on flavonoid metabolites involving in CT biosynthesis illustrated those flavonoids and three CT monomers were positively related to salt in MCs. Real-time quantitative PCR verified the genes encoding enzymes for CT biosynthesis were upregulated accordingly. Taken together, CT biosynthesis is positively correlated with Na accumulation in leaves. The CTs synthesized in chloroplasts are transported as shuttles to vacuole via cytoplasm, facilitating the sequestration and compartmentalization of excessive Na+ ions into the vacuole, which confers non-salt-secretor mangrove K. obovata a higher salt tolerance.