Eutrophication is one of the most important factors for the increasing production of organic carbon in inland waters. Variations in primary productivity across lakes due to eutrophication complicate predictions regarding future carbon burial and management of carbon sequestration in lakes. Phosphorus, an essential nutrient for plants and notorious for eutrophication, often limits primary productivity in lakes. It is crucial to normalize organic carbon burial to the content of total phosphorus (TP) in the water column to compare the inherent carbon burial capacity across lakes. However, the absence of long-term observational data of TP in lake water columns has hindered the ability to do so. In this study, we first verified that TP in sediments of Chinese lakes could substitute for that in the water column to reflect the annual primary productivity of lakes. Then we defined the inherent carbon burial potential of lakes as the total organic carbon to TP atomic ratio (TOC/TP) in the sediments. We quantified the inherent carbon burial potential of 90 lakes across China, exploring its spatial distribution, temporal trends, and potential controlling factors. The inherent carbon burial potential, based on surface sediments, decreased from western to eastern China, ranging from 466.1 to 24.3 with a mean of 137.0 ± 87.4. Mean annual precipitation was negatively related, while mean lake depth was positively related to the inherent carbon burial potential of the lakes across China. Analysis of sediment cores revealed that the mean inherent carbon burial potential of the lakes across China increased from 75.1 to 122.9 since the 1950s. Inherent carbon burial potential of the lakes in southwestern and eastern China, however, decreased since the 1990s. Changes in the extent of cultivated land in the watersheds were positively related to variations in the inherent carbon burial potential of Chinese lakes in the past few decades.