Using sediment cores to reconstruct the contamination history of per- and polyfluoroalkyl substances (PFAS) is essential for chemical management but poses challenge. Herein, sediment cores, as well as surface water and sediments were taken from two Chinese lakes to investigate the vertical distribution and migration of PFAS. Wind wave, properties of sediment and water, and chemical characters of PFAS were examined to clarify the main factors influencing PFAS migration. Total PFAS concentrations in sediment cores ranged from 0.12 to 5.28 ng g-1 dry weight (dw) in Dianchi Lake and from 0.19 to 2.51 ng g-1 dw in Taihu Lake, respectively. Strong hydrodynamic disturbance (wind-wave erosion depth up to 30 cm) in Taihu Lake resulted in consistent PFAS levels and profiles throughout the sediment core, limiting its use for retrospective analysis. In Dianchi Lake, an increasing trend of total organic carbon-normalized PFAS indicated their persistent emission in China over the past decades. Perfluorooctane sulfonic acid increased markedly from early 2000s; temporal trend in composition for perfluorocarboxylates coincided with the global production transition. Finally, we proposed a three-step conceptual framework, including lake selection, key time point assessment, and contamination history reconstruction, to further improve the reliability of PFAS retrospective analysis in lake.