Grasslands make up almost half of China's territory and are important ecological and economic areas. The native small mammals that inhabit these grasslands are often seen as pests competing with livestock and are subjected to population control. At the same time, several species are functionally important ecosystem engineers, and their removal can have far-reaching consequences for grassland health. We review the history and development of attempts to control populations of small burrowing mammals on China's grasslands from ancient times to the present day, and the relevance of these programs to grassland conservation. We describe the different methods of control in use today, and attempt to assess their prevalence and their possible effects on grassland ecosystems from a conservation perspective. Non-chemical methods are used, including manual trapping and biological control with native predators. Four rodenticides are currently registered for use on China's grasslands. Most chemical control is carried out with botulinum toxins type- C and D. We identify 41 species, across two orders (Rodentia and Lagomorpha) and seven families, which are targets of pest control. Two of these species, Marmota sibirica and Ochotona koslowi, are classed as Endangered by the IUCN. Several others are important ecosystem engineers. Case studies on the potential ecological impacts of control programs against two ecosystem engineers, zokors (Eospalax fontanierii) and marmots (Marmota spp.), are described. Finally, we give recommendations for researchers on how to approach this issue.