As an important part of the global carbon pool, lake carbon is of great significance in the global carbon cycle. Based on a study of the sedimentary proxies of Balkhash Lake, Central Asia’s largest lake, changes in the organic carbon sequestration in the lake sediments and their possible influence over the past 150 years were studied. The results suggested that the organic carbon in the sediments of Lake Balkhash comes mainly from aquatic plants. The organic carbon burial rate fluctuated from 8.16 to 30.04 g·m−2·a−1 and the minimum appeared at the top of the core. The organic carbon burial rate continues to decline as it has over the past 150 years. Global warming, higher hydrodynamic force, and low terrestrial input have not been conducive to the improvement of organic carbon sequestration in Balkhash Lake; the construction of a large reservoir had a greater impact on the sedimentary proxy of total organic carbon content, which could lead to a large deviation for environmental reconstruction. This is the first study to assess the sediment organic carbon sequestration using the modern sediments of Central Asia’s largest lake, which is of great scientific significance. The results contribute to an understanding of organic carbon sequestration in Central Asia and may provide a scientific basis for carbon balance assessment in regional and global scales.