One of the widespread impacts of climate change is the change in species distributions. In mountain ecosystems, species are shifting their distribution upslope, although a large variation exists around these responses as many species are found persisting at the trailing edge. A key hypothesis explaining this phenomenon is that heterogeneous thermal conditions from complex topography create microrefugia, allowing species to persist locally despite large-scale climate change. However, few studies have assessed distribution changes in species known to use cool microclimates, and the environmental context shaping these patterns remains unclear. In this study, we conducted a habitat resurvey of the northern pika Ochotona hyperborea, a cold-adapted species found in the mountainous areas of Hokkaido, to assess its distributional changes from the past. We also examined the drivers of their distribution by measuring habitat thermal conditions, particularly ambient and rock interstice temperatures. The habitat resurvey revealed population turnovers, with past presences shifting to absences at low- to mid-elevations, suggesting that the regional population is becoming unstable under rising temperatures. Thermal measurements indicated that rock interstices effectively buffered ambient thermal conditions, but they did not explain the distribution in low-elevations, while the presence of human land-use negatively affected the occurrence. These results suggest that the refugial effect of microclimates at the trailing edge could be overridden by other factors due to spatial hierarchy, highlighting the importance of the environmental context in which the microclimate exists for species persistence at the trailing edge.