n-Alkanes are biomarkers that are widely used as paleoenvironmental reconstruction proxies in lacustrine sediments. However, studies on their sedimentation and factors affecting sedimentation in large lakes remain relatively scarce. In this study, 120 surface sediments collected from Selin Co, central Tibetan Plateau, were used to analyze the spatial distribution of n-alkanes in a modern sedimentary system, and the factors controlling this distribution were further discussed. The sedimentary n-alkanes of Selin Co were mainly long- and middle-chain components with single or double peaks, belonging to the mixed-type input of terrestrial and aquatic plants. Leaf waxes derived from terrestrial plants in the catchment of Selin Co were the main source followed by aquatic plants, while planktonic algae living in the lake water column was a minor source, as demonstrated by their low concentration. The distribution of aquatic and terrigenous n-alkanes in the surface sediments showed a significant spatial heterogeneity; this was controlled by different factors and sedimentary processes. The distribution of terrigenous n-alkanes was mainly controlled by underwater topography; high concentrations in the sedimentary center of the east lake basin and the sub-basin in the northwest were evident. Aquatic n-alkanes were found in substantially higher concentrations in the western estuary of Zhagen River and Ali River, as well as in the southern sub-basin, Yagen Co. These distributions might be influenced by differences of geographical environment in the watershed of these main inflow rivers, as well as the intensity of sunlight, itself intensity controlled by the transparency of the water column. Although n-alkanes from the center of a lake could represent an integration of catchments in most cases, their spatial heterogeneity in large lakes like Selin Co would introduce uncertainty to paleoenvironmental reconstructions. Consequently, it is very important to investigate thoroughly the spatial distribution and controlling factors of n-alkanes in modern lake environments. It is inferred that these findings will have broad significance in large lakes similar to Selin Co, and that they will benefit studies that use n-alkanes as proxies to reconstruct past environmental changes.