Urban and cropland expansions greatly contribute to natural habitat loss. Few studies have focused on the direct and indirect impacts of urban and cropland expansions on natural habitats in Southeast Asia, a biodiversity hotspot. In this study, these impacts were quantified from 2000 to 2020 across three scales (country, ecoregion, and biome) and future Shared Socioeconomic Pathways (SSPs) (by 2030 and 2050). From 2000 to 2020, the impact of cropland expansion on natural habitats in Southeast Asia was nearly 16 times greater than that of urban expansion. The impact of cropland expansion was primarily direct, whereas the indirect impact of urban expansion was approximately 14 times greater than the direct impact during the same period. Under the 2050 SSP3 (regional rivalry scenario), the projected areas of cropland expansion reaches 113.19 × 103 km2, resulting in the most pronounced impact on natural habitats. Under future SSPs, the gap between the total impacts of cropland and urban expansions, as well as the gap between the indirect and direct impacts of urban expansion, is expected to narrow compared with current conditions. Our study suggests that natural habitat conservation efforts in Southeast Asia should address the varying impacts of urban and cropland expansions through aspects such as urban form, spatial planning, and agricultural structure.