The Tianmu Mountain National Nature Reserve (TMNNR) preserves the only primeval forest of China cedar (Cryptomeria fortunei) in the world. In order to assist in planning the protection of China cedar habitat and propose a scientific zoning project for TMNNR, we established a nature reserve geographic information system (NRGIS) of TMNNR using a geographic information system (GIS) and remote sensing (RS). In support of NRGIS, we produced a 3-dimensional simulation of TMNNR and obtained a predictive model through a combination of logistic regression modeling and multivariate analysis. The results demonstrate that slope direction, soil type, and annual precipitation are the main factors affecting China cedar habitat. The existence probability of China cedar increases with (converted) slope direction and annual precipitation. Yellow soil (FAO classification) is more suitable for the growth of China cedar in comparison to red soil (FAO classification). Finally, we predicted suitable habitats for China cedar using a model and function zoning for TMNNR. We suggest that it is necessary to analyze key factors affecting China cedar habitat in order to ensure appropriate conservation measures. NRGIS has been found indispensable for studying, protecting, and managing China cedar forest and TMN-NR. NRGIS provides not only modeling information but also the means for monitoring this rare species, identifying suitable locations for reintroduction, and carrying out visible and dynamic management of the whole reserve.