Biomass plays a crucial role in the low-carbon energy transition, with a projected contribution of 18.7% to the global energy supply by 2050. However, biofuel combustion has been a notable source of toxic mercury emissions, yet the future trends and distribution of the emissions remain inadequately understood. Here, we projected biofuel combustion under various Shared Socioeconomic Pathways (SSPs) using the Global Change Assessment Model and assessed associated mercury emissions in cooking, heating, and power generation over 2020-2050, aligning with the carbon neutrality target. Our analysis reveals that global biofuel mercury emissions are projected to be 9.90-18.40 tons by 2050, compared to the annual emissions of 13.89 tons in 2020. Notably, a substantial increase in emissions from power generation is expected, escalating from 0.57 tons in 2020 to 4.69-8.27 tons by 2050, with China and Southeast Asia emerging as primary contributors. Conversely, mercury emissions from cooking and heating are expected to decrease from 13.32 tons in 2020 to 4.40-11.53 tons by 2050, except in Africa under SSP2, where the emissions may increase from 5.91 to 6.69 tons. Our findings provide a scientific basis for policies aimed at achieving carbon neutrality targets while adhering to the Minamata Convention on Mercury. Biomass plays a crucial role in the low-carbon energy transition, but its combustion releases toxic mercury. Our study projected mercury emissions from biofuel combustion from 2020-2050 under different Shared Socioeconomic Pathways scenarios and global net-zero emissions constraints. We find that while mercury emissions from cooking and heating will decrease, emissions from power generation will significantly increase, especially in China and Southeast Asia. To achieve carbon neutrality and reduce mercury pollution, there is an urgent need for the deployment of air pollution control devices in biomass direct-fired power plants and the transformation of biomass into cleaner bioenergy should be promoted. Spatial and temporal patterns of mercury emissions from biofuel combustion across 32 country/regions under carbon neutrality are delineated Cooking and heating constituted 95.9% of mercury emissions from biofuel combustion in 2020, dropping to one-third of that level by 2050 Mercury emissions of biomass power generation rise by 7.2-13.4 times in 2020-2050, dominated by carbon capture and storage technology in 2050