We investigated historical changes in temperature and phytoplankton in Fuxian Lake (FX) and Dianchi Lake (DC), two plateau lakes in Southwest China. We detected sterols and alkyl diols as algal biomarkers (Dinoflagellates, Diatoms, Eustigmatophytes, Cyanobacteria, and Chlorophyta) in the sediment cores by using GC-MS. We characterized sedimentary organic matter (SOM) via C-13 isotope and C/N ratio, and Rock-Eval analysis to obtain total organic carbon (TOC), S2, the hydrogen index (HI), refractory carbon (RC), and nutrient status such as total phosphorus (TP) and total nitrogen (TN) in the sediment cores. The results showed that the sedimentation rates measured by ²¹⁰Pb dating ranged from 0.02 to 0.30 g cm^-2 yr^-1 and 0.07 g cm^-2 yr^-1 in FX and DC, respectively. The Bayesian isotope mixing model indicated that organic matter from plankton was the main contributor of organic matter in FX and DC and, its contents was gradually increasing . Primary productivity derived from the S2 and HI parameters showed an increasing trend in FX and DC. Cyanobacteria and Chlorophyta were the two dominant phyla in the two lakes. Algal growth was controlled primarily by temperature and nutrient availability. Principal component analysis (PCA) and multiple linear regression analysis showed that the major factors controlling the historical change in phytoplankton growth were TN and temperature in FX and DC.