The isotopic compositions of total organic carbon (TOC) in lakes have been widely used to interpret paleoclimatic changes and the depositional environments of lake sediments. However, the main factors that affect the carbon isotopes of TOG (source of organic material, water condition and others) may vary in different lake sediment records, which have limited the applicability of organic carbon isotopes in explaining biogeochemical and environmental changes in lakes. In this study, the organic carbon isotopic compositions of aquatic plants and surface sediments from Lake Qinghai and the living terrestrial plants and surface soils around the lake were systematically investigated to identify the sources of TOC in the sediments and the significance of the organic carbon isotopes of sedimentary TOG. We found that the aquatic plants in the deep water areas (>10 m) were primarily dominated by Cladophora, but submerged plants (Potamogeton and Ruppia L) are the dominant species in shallow water (<10 m). The Cladophora have negative delta C-13(org) values (-33.6 parts per thousand to -28.6 parts per thousand) that are caused by C(3-)ike photosynthesis, but the submerged plants have enriched delta C-13(org) values (-17.8 parts per thousand to -15.4 parts per thousand) that are caused by C-4-like photosynthesis. In addition, the delta C-13(org) values of Cladophora become more negative with increasing water depth because of the slow photosynthetic rate caused by the weak light intensity at depth. The isotopic data indicate that the carbon isotopes of organic material in the surface sediments are primarily controlled by the types of aquatic plant and that the delta C-13(org) values of TOC can be used to indicate the variation of the water depth (lake level). The organic carbon isotopic data from the IF core showed that the water was shallow (<10 m) because of intense evaporation related to high temperatures even though precipitation sharply increased in the warm period during the early-mid Holocene. The lake level reached its maximum level at 3 ka.