Using 76 presence-only data, altitude, percent tree cover and 11 bioclimatic variables, we modeled the geographical distribution of Macromitrium japonicum in China with an aid of a maximum entropy algorithm modeling program (MaxEnt). We found habitats suitable for M. japonicum in the major mountains in southeastern, southern, and southwestern China, and also in the Changbai Mountains, Taihang Mountains, Yanshan Mountains, Tainwan and Hainan Island. With increasing percent of tree cover, mean temperatures in the driest quarter, the warmest quarter and the coldest quarter, and with decreasing annual temperature range and mean diurnal temperature range, habitat suitability for M. japonicum increases. The MaxEnt model also indicated that areas with precipitation of the wettest month being 300 mm, and precipitation of the warmest quarter being 500–600 mm are favourable for M. japonicum. It also favours lower altitudes (0–1000 m a.s.l.), while with increasing altitude (from 1000 to 6000 m a.s.l.), habitat suitability decreases. Habitat suitability for M. japonicum firstly increases rapidly with increasing precipitation in the driest month and the coldest quarter at lower altitudes, and then slightly increases after the factors exceed a certain threshold value.