Heavy metal contamination in soil and its accumulation in rice poses a health risk to over 50% of the global population. Simultaneously, the poor management and underutilization of agricultural biomass waste presents an additional environmental challenge. Converting this biomass into biochar offers a potential solution to these challenges. This study evaluated biochar's impacts on soil trace element content, rice plant uptake, translocation, accumulation, and associated human health risks while identifying rice response mechanisms to biochar application. A two-season field experiment was conducted using five treatments: T1 (no biochar), T2 and T3 (10 and 20 tons of rice-husk biochar), and T4 and T5 (10 and 20 tons of longan biochar). Eight trace elements, categorized as micronutrients (Fe, Mn, Cu, Zn) and toxic elements (Cd, Pb, Co, Ni), were measured in rice roots, stems, grains, and soil. Biochar application reduced the heavy metal pollution index (HPI) by 5.9% to 11.4% for micronutrients and 2.8% to 4.4% for toxic elements compared to T1. Translocation, bioaccumulation, and phytoextraction indexes tend to increase with biochar, while the hazard index decreased by 5.1-9.5% for micronutrients and 1.3-8.5% for toxic elements, indicating reduced health risks. These results highlight biochar's dual role in enhancing trace element phytoextraction and reducing health risks, with a more pronounced effect on micronutrients. Rice plants responded to reduced micronutrient availability by boosting uptake while lowering toxic element absorption when HPI was high. Briefly, transforming agricultural waste into biochar for rice cultivation offers multiple benefits, promoting agricultural sustainability, environmental health, and consumer safety.