The risk assessment and source identification for potentially toxic elements (PTEs) in soils, particularly agricultural soils from megacities, are significant for environmental protection and pollution control. In this study, an intensive sampling (4127 topsoil samples and 994 subsoil samples) was conducted in the Shunyi District, Beijing, which is a suburban area with extensive cropland cover and has been impacted by the megacity over several decades. Concentrations and distributions of 8 PTEs, including V, Cr, Ni, As, Cd, Zn, Pb and Hg, were determined, and their possible sources were quantitatively assessed by principal component analysis (PCA), redundancy analysis (RDA), positive matrix factorization (PMF) analysis, and anthropogenic contribution ratio method. Among 8 PTEs, Zn, V and Cr exhibited significantly high concentrations in soils, with means of 68.29, 68.19 and 52.13 mg/kg, respectively, followed by Pb (23.84 mg/kg), Ni (22.91 mg/kg), As (8.30 mg/kg), Cd (0.15 mg/kg) and Hg (0.05 mg/kg). RDA and PCA demonstrated that the rock weathering was a significant source of V, Cr, Ni and As, and the local emissions and atmospheric deposition respectively contributed most of Cd, Zn and Pb, and of Hg in soils. This source category was confirmed the spatial variations of anthropogenic contribution ratios to individual PTEs. PMF results showed that the local emissions contributed 96.3% of Cd, 44.4% of Zn and 32.0% of Pb in soils, and the atmospheric source carrying urban pollutants amounted to 78.7–80.2% of Hg. In this case, several effective analysis methods have been successfully applied to quantify the impact of a megacity to PTEs in suburban soils. These results improve understanding of the contamination status of PTEs in suburban soils from Beijing megacity, and provide basis for policymaker regarding environmental protection and pollution control.