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Lake sediment is an important carbon reservoir. However, little is known on the dynamics and sources of sediment organic carbon in Bosten Lake. We collected 13 surface (0–2 cm) sediment samples in Bosten Lake and analyzed total organic carbon (TOC), total nitrogen (TN), stable carbon isotopic composition in TOC (δ¹³C_org), and grain size. We found a large spatial variability in TOC content (1.8–4.4 %) and δ ¹³C_org value (−26.77 to −23.98 ‰). Using a three-end-member mixing model with measured TOC : TN ratio and δ¹³C_org, we estimated that 54–90 % of TOC was from autochthonous sources. Higher TOC content (> 3.7 %) was found in the east and central-north sections and near the mouth of the Kaidu River, which was attributable to allochthonous, autochthonous plus allochthonous, and autochthonous sources, respectively. The lowest TOC content was found in the mid-west section, which might be a result of high kinetic energy levels. Our study indicated that the spatial distribution of sediment TOC in the Bosten Lake was influenced by multiple and complex processes.