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With the acceleration of urbanization, road dust poses a significant threat to ecological systems. To explore the source and ecological risks associated with heavy metals in surface dust, 36 road dust samples were collected in Beijing in May, August, and November 2018, and February 2019. The results indicated that the concentrations of Cd, Cr, Cu, Hg, Ni, Pb, and Zn exceeded their background values, and the mean concentration of Cd was nearly 10 times the background value. Three main sources were identified by Principal Component Analysis (PCA): industrial emissions, fuel combustion, and traffic exhaust. According to the Genetic Algorithm optimized Back Propagation (GA-BP) neural network, heavy metals from industrial sources and fuel combustion originate from suburban districts, while heavy metals from traffic exhaust originate from the city center. After careful screening of species and corresponding toxicity data, the concentration of pollutants corresponding to a 5% cumulative probability on the curve (HC5) of eight heavy metals was calculated by species sensitivity distribution (SSD), and the results indicate that most HC5 values are consistent with national standards. However, the HC5 values of Ni, Cu, and As differed from the national standards, which can be used to supplement existing standards. From the risk analysis based on HC5 values, the high-risk area of Ni (12.70–30.97%) was much larger than that of As (1.55–4.95%), and the proportions of high-risk areas of Ni and As reached their highest values in spring and autumn, respectively. Uncertainty existed between different geostatistical methods. The areas of uncertainty of Ni and As were small (less than 5.58%). The heavy metals in the surface dust in Beijing had potential ecological risks that vary with seasons and regions. Therefore, it is critical to implement targeted management measures based on pollution sources and risk distribution. [ABSTRACT FROM AUTHOR]