Internal P loading (IPL) is a severe problem for the remediation of eutrophic lakes that the release of sedimentary P impedes the reduction of P in the lakes. To control the IPL, in-situ capping is a widely used remediation to improve the P burial efficiency. However, a lack of study has been done to investigate the long-term climate change effect on the P burial and release mechanisms. Thus, we thoroughly investigated the evolution of the P accumulation and release in the sediment of Dianchi Lake, a eutrophic plateau lake. The stability of sedimental P, which determines the internal P loading, is predominantly affected by climate change, anthropogenic activities, and the macrophyte-to algal-dominated ecosystem transition. The sediment core indicates more Ca accumulated in the 1930s caused by climate change and corresponding biological responses resulting in the transition of stable P fractions, which generates a vulnerable ecosystem from eutrophication. The self-clarification helps the lake accumulate anthropogenic P pollutants in the sediment as stable forms until the degradation of the ecosystem. It shows the NaOH extractable P (NaOH-rP) and HCl-extractable P (HCl–P) preservation capacity in an algal-dominated lake decreases from 780 to 700 mg cm−2•a−1 to 170 and 270 mg cm−2•a−1 respectively. The most stable P fraction (Res-P) is predominantly affected by climate change rather than human activities that a constant reduction from 730 mg cm−2•a−1 to 70 mg cm−2•a−1 after the climate change event that subdued the microbial activity producing Res-P in the 1930s. The spatial distributions of P fractions imply that the macrophyte-dominated area has more efficiency in preserving stable P in the sediment, thus the restoration of macrophyte as well as the benthonic microbe community should be considered in the remediation engineering.