The formulation of reasonable concentration classification standards can significantly enhance the protection of populations against atmospheric heavy metals, and the development of these standards should be grounded in national-level probabilistic risk assessment to establish multiple grading benchmarks. In this study, the probabilistic health risk assessment model was used for the first time to assess the health risks of hazardous metals [arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), and vanadium (V)] based on a publication dataset containing 57,737 PM2.5-bound heavy metal samples from China. Our results showed that the average non-carcinogenic risk attributed to heavy metals in all provinces of China was less than 1. In contrast, the average carcinogenic risk was greater than 10–6 in all provinces. The logarithmic mean non-carcinogenic health risks for the eight non-carcinogenic metals were ranked as follows: V (− 1.55 ± 0.96) > As (− 1.79 ± 0.96) > Mn (− 1.84 ± 0.82) > Co (− 2.05 ± 0.89) > Cd (− 2.14 ± 0.94) > Ni (− 2.59 ± 0.92) > Cr (− 3.26 ± 0.93) > Hg (− 4.86 ± 0.91), while the logarithmic mean carcinogenic health risk for the seven carcinogenic metals was Cr (− 5.33 ± 0.93) > V (− 5.79 ± 0.96) > As (− 5.98 ± 0.96) > Co (− 6.32 ± 0.89) > Cd (− 6.89 ± 0.94) > Pb (− 7.02 ± 0.93) > Ni (− 7.22 ± 0.92). The metals that contributed most to the non-carcinogenic and carcinogenic risks were V (35.86%) and Cr (57.61%), respectively. Through probabilistic risk assessment, we constructed seven-level health benchmarks for carcinogenic metals (As, Cd, Co, Cr, Ni, Pb, V). These benchmarks of extremely low health risk for the seven carcinogenic metals (As, Cd, Co, Cr, Ni, Pb, V) were 0.00037 μg/m3, 0.0011 μg/m3, 0.00012 μg/m3, 0.00011 μg/m3, 0.0043 μg/m3, 0.025 μg/m3, and 0.00031 μg/m3, respectively. Overall, this study is the first nationwide comprehensive assessment of the probabilistic risk of atmospheric PM2.5-bound toxic metals and provides a theoretical basis for revising and improving China's air quality standards.