The rate of organic carbon (OC) burial in lakes depends considerably on natural and anthropogenic factors. Delineating how and to what extent potential drivers shape a lake’s OC burial rate is crucial for anticipating OC sequestration under future environmental change scenarios. Alpine lakes provide valuable opportunities for studying the influence of climate warming and atmospheric nitrogen (N) deposition on OC burial in lakes, owing to the lack of human activities in their catchments; however, this aspect has not been sufficiently documented. Here, the OC burial rate was reconstructed in two alpine lakes (Heihai and Jiren) from the southeastern margin of the Tibetan Plateau over the past ∼ 160 years, and the associated drivers were identified by resolving the temporal trends in organic matter (OM) input from specific sources to lake sediments via paleolimnological methods. The results demonstrated a consistently low OC burial rate (6.21–10.86 g m−2 yr−1) in Lake Heihai. The low hydrogen index (HI), moderate Paq, and high long-chain n-alkane flux revealed that submerged macrophytes and terrestrial plants are major contributors to the sequestrated OC. The notable decrease in the OC burial rate after 1980 was hypothesized to be caused by regional climate warming during this period because a greater export of terrestrial materials under such a climate can inhibit light penetration, diminishing submerged macrophyte productivity and OM input. In contrast, the synchronous input of higher amounts of terrestrial plant OM was largely degraded owing to the increased water temperature and the intensification of water column stratification. In Lake Jiren, a notably high OC burial rate (13.82–46.75g m−2 yr−1) was observed. The high HI, Paq, and short-chain n-alkane flux showed that phytoplankton and submerged macrophytes were the major contributors to the sequestrated OC. The two-phase increase in the OC burial rate in this lake, including a slow increase after 1947 and a rapid increase after 1983, might have resulted from strengthening aquatic primary productivity and OM input, driven by anthropogenic intensification of nutrient emissions, especially reactive N, from highly urbanized areas and the subsequent long-term atmospheric transport and deposition of these materials over the lake basin. A comparative analysis of the results between the two lakes suggested that atmospheric N deposition has a stronger influence on the OC burial than climate warming. These drivers affect the OC burial rate by altering aquatic productivity rather than the terrestrial OM input. This study provides a basic for predicting future OC burial scenarios in warmer climates with more intense anthropogenic N emissions.