To satisfy their requirements for food and safety, animals need certain habitats to live. Marmots generally select habitats with certain elevation, land surface temperature, soil and vegetation type, and certain mountain slope and aspect; however, what habitats are needed at relatively smaller scales are poorly known. The Himalayan marmot (Marmota himalayana) is distributed mainly on the Qinghai-Tibet Plateau, a region exhibiting diversified topographic features, and the Zoige wetland in the northeast part of the plateau is also the home of the Himalayan marmot. The region is famous for its plateau peat bog, and the suitable habitats for Himalayan marmots are patchily distributed in the wetland. To investigate what kinds of patches are preferred by the marmot in this wetland ecosystem, we measured and compared the soil and vegetation characteristics of used and unused patches. We found that unlike factors governing the habitat selection at macroscales, patches characterized by flat ground and low soil moisture content, with medium vegetation standing height and low vegetation density, are selected in the Zoige wetland. Patches of this kind are selected to meet the marmots' requirements for burrow construction and predator avoidance in such a wetland ecosystem. Together with previous studies on habitat selection of the marmot species at macroscales, we showed that to explore how the animals survive in an environment, it is important to conduct the analysis at multiple scales.