Deforestation is a major environmental issue driving the loss of animal and plant species. Afforestation has recently been promoted to conserve and restore Chinese forest ecosystems. We investigated the distribution of small-mammal assemblages in an area where forest and associated deforestation habitats dominate and in an agricultural area where afforestation is ongoing in the Loess Plateau of southern Ningxia Autonomous Region, P.R. China. Multiple trapping was used. Assemblages were defined based on the multinomial probability distribution and information theory. Species turnover between assemblages of deforested and afforested habitats was high, although no clear effect on species richness was observed. The two assemblages described along the deforestation gradient displayed higher diversity, whereas diversity was lower in assemblages identified in afforested habitats where Cricetulus longicaudatus, known agricultural pest in various areas of China, clearly dominated. The threatened Sorex cylindricauda and Eozapus setchuanus were recorded along the deforestation gradient but not in plantations. Therefore, habitats present along a deforestation succession in this part of Ningxia sustain a high diversity of small mammals and include species of conservation concern. At the present stage of its process (maximum 15 years), afforestation in southern Ningxia favours the dominance of an agricultural pest.