A new innovative methodology system framework for source apportionment and source-specific risk assessment has been proposed and actively applied to identify the contamination characteristics, oriented sources and health risks associated with contamination levels of Heavy metals (HMs) and Polycyclic Aromatic Hydrocarbons (PAHs) in soils, a typical cold agricultural region in Northeastern China. To achieve this meaningful goal, a large-scale dataset including 1780 top soil samples, 10 HMs and 16 priority PAHs has been organized and collected from a typical study area in China. The total concentrations of the 10 selected HMs in study area range from 0.05 to 2147.40 mg/kg, with an average of 549.25 ± 541.37 mg/kg. The average concentrations of PAHs for (3–6)-rings are 16.60 ± 18.90, 26.40 ± 28.20, 9.51 ± 13.00 and 1.99 ± 5.30 ng/g, respectively. On the base of optimized literature source fingerprints for HM and PAH, a widely used receptor model, positive matrix factorization (PMF) has been applied to apportion the contamination sources HMs and PAHs in soils. Then source-specific health risk of soil HMs and PAHs have been assessed using the probabilistic incremental lifetime cancer risk model incorporated with source apportionment results data. Fertilizer residues/coke oven comprise the primary contamination source contributors of HMs and PAHs with corresponding contributions of 32.23 % and 27.93 % for HMs and 37.94 % for PAHs. Fertilizer/pesticide residues contributes most to the risks of soil HMs (28.8 %), followed by fossil fuel combustion (24.6 %), mining activities (20.2 %), traffic and vehicle emission (16.3 %) and electroplating/dyeing (14.1 %). Meanwhile, the ranking of health risks from the five identified contamination sources of soil PAHs are resident discharge, coal-fired boilers, coke oven emission, gasoline combustion and power plant, with the contribution of 27.1 %, 25.3 %, 17.3 %, 15.5 % and 14.8 %.And relatively, source-specific risk assessment demonstrates fossil fuel and coal combustion contribute the greatest impact to the total risk of HMs and PAHs (61.7 % and 56.1 %), respectively. This study provides a good example of how the source specific health risk assessment can be utilized to reduce the contamination in soils.