Human activity is increasingly and persistently disturbing nature and wild animals. Affected wildlife adopts multiple strategies to deal with different human influences. To explore the effect of human activity on habitat utilization of the Himalayan marmot (Marmota himalayana), habitat utilization patterns of three neighboring marmot populations in habitats affected differently by human activities were recorded and compared. We found that: (1) Distance between reproductive burrows becomes shorter under the influence of human activity, and further, the more disturbance a population suffers, the more burrows were dug as temporary shelter to reduce the distance to those shelters when threatened. More burrows that are closer in the disturbed habitats improve ability to escape from threats. (2) Burrow site selection is determined by the availability of mounds in the habitat. Breeding pairs selectively build burrows on mounds to reproduce, potentially to improve surveillance and the drainage of their burrows. Human activities generally drive breeding pairs away from the road to build their reproductive burrows, likely to reduce disturbance from vehicles. However, even heavy human activity exerts no pressure on the distance of reproductive burrows from the road or the mound volume of the high disturbance population, potentially because mounds are the best burrowing site in the habitat. Marmots deal with nonlethal human disturbance by digging more burrows in the habitat to flee more effectively and building reproductive burrows on mounds to gain better vigilance and drainage efficiency.