Sedimentary organic matter is an important component of the metabolism of a lake’s ecosystem, and it is generally derived from both the watershed and the primary productivity of a lake. Understanding the sources of organic matter in lakes and lake trophic status is important when evaluating the quality of lake ecosystems. We summarize the spatial distribution of total nitrogen (TN), total organic carbon (TOC), TOC/TN (C/N) molar ratios, and organic carbon isotope (δ13Corg) of the surface sediments of Fuxian Lake, Yunnan–Guizhou Plateau, Southwest China, which is the second deepest freshwater oligotrophic lake in China. The results show that the distributions of TN, TOC, C/N, and δ13Corg of the surface sediments are spatially heterogeneous, which is also the case for the trophic conditions of the lake. Compared with the adjacent eutrophic lakes and typical lakes in other areas with strong human activities, the content of organic matter is at a low level. Meanwhile, the autochthonous organic carbon in the surface sediments was characterized by lower δ13Corg (−25.3~−28.5) and C/N (8.7~12.9), suggesting that the biological carbon pump effect plays a significant part in the stability of carbon sinks by coupling with carbonate weathering. Our results emphasize the importance of the carbon sink of coupled carbonate weathering and aquatic photosynthesis in the evolution of the carbon cycle in lakes. Although modern monitoring shows that Fuxian Lake is an oligotrophic lake, there are potential risks of organic nitrogen pollution with respect to surface sediments, especially in northern and southern shallow-water areas. The organic pollution of lakes can be reduced by controlling the discharge of wastewater and reducing the nutrient loading of agricultural runoff.