Anthropogenic climate change and unreasonable land use have exacerbated desertification in recent decades. However, the biotic-environmental regulatory mechanisms for the temporal stability of desert ecosystems in the marginal areas around mobile deserts, as critical ecological safety barriers to restrict the development of desertification, are still less understood. Based on extensive field sample plot survey data and spatial data, we comprehensively assessed the contribution and driving mechanisms of biotic (vegetation pattern and species diversity) and environmental (climate, soil, spatial location and terrain) drivers to the temporal stability of gravel desert ecosystem (GDE) and sandy desert ecosystem (SDE) around the Badain Jaran Desert and Tengger Desert in Northwest China. Our results showed the temporal stability in GDE was driven by plant species diversity, and climate played an indirect role by influencing plant species diversity. The temporal stability of SDE was mainly regulated by environmental variables, with climate and soil properties directly affecting it, rather than indirectly through biotic variables. A trade-off existed between the temporal stability of SDE and vegetation productivity, which was absent in GDE. Our findings highlight the divergent biotic-environmental mechanisms underlying the temporal stability of GDE and SDE at the margins of mobile deserts. Based on these insights, we propose targeted conservation strategies for two major desert ecosystems: for GDE, focus on protecting and restoring vegetation diversity; for SDE, prioritize sand fixation and soil improvement. These results provide crucial theoretical guidance for desertification control and the sustainable management of desert ecosystems.