Global climate change has an important impact on the structure, function and process of global ecosystems, affecting all aspects of economic and social development. Analysis of factors affecting carbon reserve in natural ecosystems has become an important part of climate change research. An analytical method for influencing factors of carbon reserve in natural ecosystem under spatiotemporal dynamics is proposed in this paper. Based on six national inventory data of natural ecosystem resources from 1973 to 2003, the relationship between average net radiation and temperature and precipitation in China is evaluated by using Chikugo model and comprehensive model. Using factor analysis method, the impact of climate change factors on carbon reserve in natural ecosystem is judged. Based on the measured biomass data of natural ecosystem, the dynamic changes of carbon reserve of natural ecosystem in China since 1970s are estimated by using the biomass-accumulation fitting relationship of tree species and age groups. The results show that climate change, spatial distribution of natural ecosystems and human activities have important impacts on carbon reserve in natural ecosystems.