The widespread and high use of biomass fuels (BF) by farmers contribute to air pollution-associated health impacts. However, the toxicity and spatial health risks of heavy metals in PM2.5 from BF burning, especially for elements (Cr, As, Cd, Hg, and Pb) listed as hazardous air pollutants (HAPs) in China, remain unknown on the national scale. This study tested the emission factors (EFs) of 18 heavy metals in PM2.5 for 23 BF sources throughout China. Then, complete emission results for heavy metals in PM2.5 from BF burning in China were estimated using the measured EFs and a field survey. Finally, the GEOS-Chem and Risk Quotients models were utilized to calculate the spatialized health risks from heavy metals in PM2.5 for the first time, including the gridded hazard index (HI) and carcinogenic risk (CR). Overall, the measured total EFs of 18 heavy metals in PM2.5 for 23 BF sources ranged from 5.13 mg kg−1 to 24.14 mg kg−1, and the sum EFs of hazardous elements (Cr, As, Cd, Hg, and Pb) varied from 0.45 mg kg−1 to 7.26 mg kg−1. The results indicated that the emissions of Fe, Zn, Pb, Cd, and Cu in PM2.5 from BF burning were the highest, with emissions of 1440.4, 801.8, 434.8, 399.5, and 397.4 Mg, respectively, in 2014. The emissions of other hazardous elements (Cr, As and Hg) in PM2.5 from BF burning were 203.7, 68.67, and 6.36 Mg, respectively. Compared with other anthropogenic sources, the emissions of As (66.7 Mg) from domestic coal burning were similar to those from BF burning, while the emissions of Cr (98.7 Mg) and Cd (102.7 Mg) were much lower for coal. Former studies might have underestimated the toxicity of Cr, As, and Cd by ignoring the emissions from BF burning. Spatially, the hazardous elements exhibited higher emission intensities in the Sichuan Basin, Northeast China Plain, and North China Plain, which exceeded 200, 55, 350, 5 and 350 g yr−1 for Cr, As, Cd, Hg, and Pb, respectively. The monthly emissions of hazardous elements were the highest in winter (January, February, and December), accounting for 41% of the total emissions. On the national scale, the gridded health risk of hazardous elements attributable to BF burning exhibited a relatively high level and spatial heterogeneity. The national HI for children (≤2.8 × 10−2) and adults (≤1.5 × 10−2) were all far lower than the acceptable level (HI ≤ 1). However, the CR in rural areas of Shanxi, Hebei, Beijing, and Henan (1 × 10−6 to 2.7 × 10−6) reached 2.7 times higher than the acceptable level (CR ≤ 1 × 10−6). These results highlighted that when aiming to mitigate the heavy metals exposure risk in the general population, BF burning emissions should be carefully considered. The governments should improve the awareness of the toxicity and health risks from BF burning. which may reduce the willingness of farmers to use BF sources and further promote the rural energy transition and utilization systematically.