Forestry practices can lead to changes in wildlife habitat that could have lasting effects on the distribution of species. Hence, the aim of this study was to determine the effects of forestry practices on habitat variables and habitat use by mammals in three different stands (control, clear-cut and clear-cut with reserves) in a Japanese larch Larix kaempferi plantation from April to October in 2016 and 2017. We recorded the presence of field signs for the following six mammal species: Korean hare Lepus coreanus, raccoon dog Nyctereutes procyonoides, Eurasian badger Meles meles, water deer Hydropotes inermis, roe deer Capreolus pygargus and wild boar Sus scrofa. Habitat variables significantly differed among three stands. Field sign (feces, foot prints and feeding signs) abundances of mammals showed significant differences between the control and clear-cut stands. Moreover, field sign abundances of all species were highest in the clear-cut with reserves stand. We calculated the impact of clear-cutting on habitat use by mammals using GLMMs. Both clear-cutting in the models were significant and had positive coefficients on habitat use by Korean hare, raccoon dog, deer and wild boar. In Eurasian badger models, only clear-cutting with reserves show positive impacts on habitat use. Habitat selection by forest edge species such as Korean hare and deer showed dependence on understory structure. Abundant understory in the clear-cut with reserves stand may not only provide vegetative food and cover for herbivores but also small prey species for omnivores and carnivores. The results of our study show that forest understory is one of the most instrumental factors mitigating the effects of clear-cutting on habitat use by mammal and it should, therefore, be given due importance in forestry practices.