Carbon burial patterns in lakes and their dynamic changes significantly impact terrestrial carbon sink fluxes and global carbon budgets. In this study, multi-indicator analysis of sediment core samples (P1, P2, and P3) from Pipahai Lake was conducted. Integrating the chronological sequences of 210Pb and 137Cs, we identified the historical changes and spatial characteristics of total organic carbon (TOC) and inorganic carbon (TIC) burial in Pipahai Lake since 1884. The results show that the TOC content was higher than that of the TIC. They exhibited an increasing trend with decreasing depth. Linear regression results indicated that the variation of TOC is less directly affected by precipitation (R = 0.39) and temperature (R = 0.58), while temperature may have a greater impact on TOC. From 1884 to 1995, nutrients were not the primary factor influencing changes in TOC. The synchronous variation in TIC and TOC contents reflects a higher contribution of external inputs to carbon burial in the Pipahai Lake basin. After 1996, nutrients may have begun to affect variations in TOC. The TOC primarily originates from distal aeolian transport or autochthonous sources, though human activity has played a role in its evolution. The TIC content is controlled by the TOC content and autochthonous sources. This study will contribute to the understanding of the carbon cycling dynamics and their influencing mechanisms in a high-altitude lake ecosystem.