Connectivity is crucial for species conservation, but most assessments define connectivity solely in terms of protected or natural areas and land covers without regard for the underlying thermal environment. As climate change accelerates, it is becoming increasingly important to not only assess land use and land cover changes (LULCC) but also how surface temperatures are evolving and creating more fragmented thermal refuges over time. This research investigates how the surface thermal environment has changed over time in Phoenix, Arizona, USA, a desert city in the southwestern United States, and how the spatial patterns of cooler refuges within the heat landscape, or “heatscape,” may be affecting wildlife habitat availability alongside LULCC. We quantify the structural and functional connectivity of thermal refuges using a suite of connectivity metrics from landscape ecology to demonstrate how the spatial distribution and configuration of these critical areas has changed over the last 35 years and what the implications are for the many wildlife species living in this desert environment. Results show that thermal refuge patches have been shrinking and becoming more fragmented over the past 35 years, with connectivity also declining over the same period. A key inflection point was identified in 2000, when the probability that cooler refuges patches were connected dropped to nearly zero, and it has remained at that low level ever since. These shifts in connectivity are tightly coupled with LULCC in the study area, particularly the loss of irrigated agriculture as it has been replaced by residential and other developed land uses over time. Decreasing water security in the region also threatens to reduce the availability of cooler patches and, simultaneously, the connectivity of those refuges. Introducing cooler patches through engineered materials or artificial shade may help offset some of the losses from irrigated lands. The findings offer a perspective for conservation research with implications for advancing a more formal thermal landscape ecology for understanding and improving the relationship between spatial thermal patterns and ecological processes.