An increasing number of nature reserves are being invaded by various development and construction activities, such as energy, resources, and transportation facilities. The ecological footprint model, which enables a quantitative assessment of ecological sustainability, can assess whether human consumption at various spatial scales falls within the regenerative capacity of the biosphere. Based on the traditional ecological footprint evaluation model: the Global Agro-Ecological Zone (EF-GAEZ model), this study proposes an improved ecological footprint model based on net primary productivity (EF-NPP model) and its validations. In this study, the status of ecological footprints and the ecological carrying capacities of 319 national nature reserves in 2010 is explored, and the changes in ecological surpluses and ecological deficits from 2000 to 2010 are analyzed. The ecological footprint per capita and the ecological carrying capacity per capita calculated by the two models were mostly consistently at the same level (more than 68%), which indicated that the ecological footprint per capita and the ecological carrying capacity per capita of the two models followed the same rule. The EF-NPP model can reflect the change in the global climate, the degradation of the soil, and the progress of the technology.