Multiple organic proxies and lipid biomarkers in the sediment core samples collected from Luoma Lake and Hongze Lake in Jiangsu are used to expound the relationships of global warming with lacustrine productivity and depostion of polycyclic aromatic hydrocarbons. Total organic carbon, S2, and hydrogen index in sedimentary organic matter were obtained with the Rock-Eval analysis. Nutrient status such as total phosphorus and total nitrogen was measured in the sediment cores. The source apportionment modeling and statistical analyses demonstrated that algal organic matter and bacteria organic matter showed an increasing trend and an obvious enrichment effect on PAHs, which was also related to the increasing temperature and algal productivity in the lakes. Global warming enhanced the lacustrine productivity and the accumulation of polycyclic aromatic hydrocarbons. The rapidly increasing ecological risks of PAHs in LM and HZ indicated the impact of global warming and human activities in the last 60 years. Therefore, the internal cycling and the input of contaminants and nutrients in the lakes should be controlled to reduce the algal growth in LM and HZ.