Disentangling the role of natural and anthropogenic factors is a major challenge in paleofire studies. Here, we introduce the molecular biomarkers of polycyclic aromatic hydrocarbon (PAHs), combined with charcoal and black carbon in sediments of archaeological sites, to identify anthropogenic signals of environmental change during the middle Holocene. In the prehistoric period, an intensified-fire regime period, inferred on the basis of PAHs, char and macro-charcoal levels, has been attributed to intensified anthropogenic biomass burning from dry crop cultivation between 6500 and 5000 and 3900–3600 yr BP., corresponding to the earliest Chinese settlements during the Miaodigou & Banpo IV Culture and the development of the Erlitou Culture under drier climate conditions. Subsequently, the fire frequency decreased notably between 4500 and 4000 yr BP. as the climate became wetter and there were shifts in the frequency of high-magnitude floods, corresponding to the abandonment of late Neolithic settlements in the floodplain. Changes in the PAH fluxes in sediments are positively correlated with intensified-fire regime periods, consistent with the charcoal and black carbon fluxes during those periods. Principal component analysis of PAH fluxes suggests that these intensified-fire events have a pyrogenic signature, implying that the PAHs were derived from biomass burning of fuelwood and other woody plants. In this study, PAHs in loess sediments have been used as the indicators of anthropogenic biomass burning through time. Meanwhile, PAHs also record the shift of modes of production and the evolution of human settlements as well as the choices made in response to limited natural resources. To comprehensively analyze the paleofire records of PAHs, charcoal and black carbon combined with multiproxy evidence are needed to understand wildfire history as well as human land use and social and cultural development across the study regions in depth.