This article is focus on the distribution and source of organic matter in tidal flat in the Jiulong River Estuary, and to seek effective organic geochemistry proxies for recognize sedimentary microfacies, and thus to help that organic carbon is better applied to identify sedimentary microfacies and paleo-environment. Forty one surficial sediment samples were obtained and measured their grain size, total organic carbon (TOC), total nitrogen (TN), and organic carbon stable isotopes (δ¹³C) in the tidal flat from three sedimentary environments: upper tidal flat, middle tidal flat and lower tidal flat in summer and winter. The results show that, from upper tidal flat to lower tidal flat, the grain size of sediments becomes coarser gradually with decreasing TOC, TN and C/N, and the increase of δ¹³C. The sources of organic matter in the upper tidal flat are dominated by terrestrial organic matter and mangrove, marine organic matter and Spartina alterniflora in middle tidal, and marine organic matter in lower tidal flat. The distribution and sources of organic carbon in tidal flat from the Jiulong River Estuary are controlled by the seasonal changes of land-ocean interaction, sedimentary hydrodynamic sorting, and plants. There is a significant difference in TOC, and a highly significant difference in TN and δ¹³C in sediments of the tidal flat. We thus proposed that organic geochemistry properties TOC, TN and δ¹³C are the effective indicators to identify upper tidal flat and middle-lower tidal flat in the Jiulong River Estuary.