Balancing biodiversity conservation and food security is the key to global sustainable development. However, we know little about the future global conflict risk hotspots between biodiversity and food security at both country and Biodiversity Hotspots (BHs) levels. First we calculated land use intensity index (LUII) based on future land use simulation, incorporated data on species richness(including birds, mammals and amphibians) and introduced the Global Food Security Index (GFSI). Then we used local indicators of spatial association (LISA) and bivariate choropleth map to identify the future global conflict risk hotspots between biodiversity conservation and food security. These include 10 countries (including Congo (Kinshasa), Sierra Leone, Malawi, Togo, Zambia, Angola, Guinea, Nigeria, Laos, Cambodia) and 7 BHs (Eastern Afromontane, Guinean Forests of West Africa, Horn of Africa, Indo-Burma, Mediterranean Basin, Maputaland-Pondoland-Albany and Tropical Andes). Special attention needs to be paid to these hotspots to balance biodiversity conservation and food security.