With economic development and population growth occurring throughout China, there has been increasing conflict between resources, environmental protection and economic development in a number of regions. Therefore, it is important to correctly evaluate the pressure of human activities on the natural environment and the ecosystem carrying capacity at a regional scale. The ecological footprint model has received much attention as an indicator of regional sustainable development. Recent studies investigating the ecological footprint of regions in China have focused on the city of Nanjing, due to the speed of urbanization and the rate at which built-up areas are expanding in the city. Thus, based on the ecological footprint model to study per capita ecological footprint and ecological carrying capacity in Nanjing from 1999-2009, this paper applied the Mann-Kendall method to analyze the abrupt change point of per capita ecological footprint in Nanjing. The Mann-Kendall method is a non-parametric statistical test, which has the advantages of a wide range of detection, a small human impact and a high degree of quantification. In light of three subsystems-economic, social and ecological-we selected 14 indices and employed the gray indigence method to explore the reasons of per capita ecological footprint variation in Nanjing between the two different phases, from 1999-2002 and from 2003-2009. The results show that during the period between 1999-2009, per capita ecological footprint generally grew; the change of per capita ecological capacity and per capita ecological deficit had a decreasing trend; the unit of 10,000 in GDP's ecological footprint and ecological diversity index dropped gradually; the eco-ecological system development capacity improved; but ecological pressure remained significant. The variation of per capita ecological footprint in Nanjing is divided into two stages: low-level growth stage, which is from 1999-2002, and high-level fluctuation stage, which is from 2003-2009. From 1999-2002, the main factors influencing per capita ecological footprint were the primary industry production value, population density, and the green coverage rate of built-up areas. While from 2003-2009, the main factors influencing per capita ecological footprint were the proportion of tertiary industry production value in GDP, rate of sewage treatment, and per capita greening area. Through comparative analysis on the ecological footprint evolution of different phases in Nanjing-from 2003-2009 and from 1999-2002-we found that the economic subsystem was still acting as the main function, but the main influencing factor had transformed from agriculture to tertiary industry. At the same time, the influences of the ecological and social subsystems had been upgraded because the degree of correlation between per capita ecological footprint and various evaluation indices (per capita housing living space and population density in social subsystem, rate of sewage treatment reflecting treatment ability of waste, and per capita greening area reflecting the level of greening in ecological subsystem) had increased. In addition to our findings, we propose a suite of sustainable development policies that aim to help in optimizing industrial structure, controlling the population, strengthening infrastructure construction, improving the resident-inhabited environment, increasing the construction of urban greening, improving the capacity of dealing with pollutants, and decreasing pollutant discharge.