Historical polycyclic aromatic hydrocarbon (PAH) pollution was explored through the sedimentary records of three lakes: Huguangyan Maar Lake (HGY) in South China, Mayinghai Lake (MYH) in North China, and Sihailongwan Lake (SHLW) in Northeast China. In these three lakes, the PAH concentrations in sediments are still rising, showing the different trend to lakes in developed countries. PAH pollution in South China occurred from 1850, much earlier than the increases since 1980 observed in North and Northeast China. The temporal trends of PAH concentrations in lake sediments are highly correlated with local economic development. Spatially, although the region where HGY is located has the highest gross domestic product, higher fluxes of PAHs were found in MYH sediments, indicating that atmospheric PAH pollution in North China might be more serious, and that PAH pollution is not fully correlated with economic development. Source analysis suggested that the PAHs in lake sediments are mainly derived from oil leaks, coal and biomass combustion, vehicle emissions, and diagenesis. Positive matrix factorization (PMF) model revealed that the contribution of vehicle emissions and coal combustion to PAHs has increased significantly in the past 40 years. Benzo(a)pyrene equivalent (BaPE) in the surface sediments of MYH and SHLW were similar and higher than in HGY. In HGY, vehicle emissions posed the highest toxic risk, followed by coal combustion. However, in MYH, the toxicity risk of vehicle emissions was close to that of coal and biomass combustion due to the highly developed coal industry in Shanxi Province. In SHLW, the contribution of fossil fuel combustion to BaPE was significantly higher than that of biomass combustion. This study provides important information for understanding PAH pollution affected by anthropogenic activities in the Anthropocene and provides a scientific basis for formulating PAH pollution control strategies.