Rodents play an important role in rangelands through the engineering of extensive burrow systems, which provides key habitats for many animal and plant species. We have analyzed the long‐term variation in the abundance and distribution of rodent burrows in grazing ecosystems of southern Russia (Kalmykia) under the landscape change from desert to steppe caused by the drastic reduction of livestock after the collapse of the USSR in the early 1990s. We conducted burrow surveys in the “desert” (1980) and “steppe” (2017) periods on 19 3‐km transects. We found considerable changes in burrow abundance and distribution, as well as evidence of desert habitat fragmentation and isolation caused by the expansion of tall‐grass communities. Burrows of the open‐dwelling diurnal ground squirrel (Spermophilus pygmaeus), the dominant and the keystone species during the “desert” period, almost completely disappeared from the rodent burrow network by 2017, indicating significant habitat loss. In contrast, the burrows of the folivorous social vole (Microtus socialis) which was rare in the 1980s, became abundant and ubiquitously distributed. The burrow density of the desert‐dwelling psammophilous midday gerbil (Meriones meridianus) decreased, while the distances between occupied patches increased, indicating desert habitat fragmentation and loss of population connectivity. Burrows of the folivorous tamarisk gerbils (M. tamariscinus) were recorded only sporadically in both 1980 and 2017. The observed changes in the rodent burrow network, the key component of grazing ecosystems, correlate with rodent species ecology and can have long‐term and important consequences for ecosystem functioning.