Marmota, a key host for the plague in China, plays a crucial role in the transmission and spread of this deadly disease. As climate change continues to alter environmental conditions, the spatial distribution of Marmota populations is also expected to change. These changes may, in turn, affect the dynamics of plague transmission and create new areas of risk for humans. To explore this effect, this study aims to assess the impact of climate change on the distribution of Marmota and identify potential spatial and temporal overlaps between Marmota habitats and human populations in the future. To achieve this, the study employed the Maximum Entropy (MaxEnt) model to analyze 43 environmental variables that may influence Marmota's spatial distribution. These variables included bioclimatic, topographic, soil, and vegetation data. Twenty-two of the 43 variables were selected for modeling through Spearman's correlation analysis and the knife-cut method. The study then used these variables to predict the future distribution of Marmota under three Shared Socioeconomic Pathways (SSPs)—SSP126, SSP245, and SSP585—during two timeframes: the 2050s and the 2070s. Potential migration pathways of Marmota under different future climate scenarios were simulated using the Minimum Cumulative Resistance (MCR) model in conjunction with future land use projections. The results revealed that the current Marmota habitat spans approximately 147,000,0 km2, primarily in the western and southern regions of Xinjiang, central and eastern Tibet, eastern Qinghai, western Sichuan, and southwestern Gansu. Under different climate scenarios, the Marmota's habitat is expected to expand or contract, with central Tibet, western Sichuan, eastern Qinghai and southern Xinjiang expected to be its main migratory passages. The study also identified areas of risk for Marmota-human overlap, which are mainly located in the northern, southern, and western edges of Xinjiang, central and eastern Tibet, eastern Qinghai, western Sichuan, and southwestern Gansu. These risk zones are likely to change under various climate scenarios, with changes in land-use types having a greater impact on shifting risk zones under short-term and low CO2 concentration emission scenarios, while climate change dominates under long-term and high CO2 concentration emission scenarios. This research underscores the complex interplay between climate change and land use in shaping the future distribution of Marmota populations and the associated risk for plague transmission. The study's findings are crucial for developing effective monitoring and management strategies aimed at controlling the spread of plague, particularly in regions where Marmota populations overlap with human settlements. By providing a detailed assessment of future Marmota habitat changes and identifying high-risk areas, this research offers valuable insights that could inform public health and conservation efforts in the face of a changing climate.