Ecological security is an interdisciplinary of natural science and social science. There is still no an internationally accepted definition of ecological security at present. In this paper, ecological security model of Three Gorges Reservoir in Chongqing was established using system dynamics. Firstly, according to special geographical features of Three Gorges reservoir, an improved DPSIR model, which involves all aspects of society, economy and environment, was applied to establish an evaluation index system of ecological security. AHP method with objective and subjective combination characteristics was selected to endow these indices weight. Secondly, based on the ecosystem characteristics of Three Gorges reservoir, a system dynamics model containing economy, population, and environmental subsystems was developed. The model was set up using specialized software VensimPLE and data from "Chongqing Statistical Yearbook 2001-2007" for population, GDP, and the amount of environmental pollution. Main parameters and their mutual feedback relationships in the model were determined. GDP, the total population, the amount of environmental pollution were selected as the main variables; grain output ratio, forest coverage rate, soil erosion rates and other indicators were selected as the important factor parameters; the area of soil erosion, Net-GDP, pollution treatment rate were selected as the evaluation factors. Meanwhile, historical and simulated values were compared to verify this model. The comparison of results from calibration and observation shows that the model corresponds to observed behaviors, and the simulated values fit well with the observed data and changing trends. Moreover, 3 scenarios named sustainable development, resource exhaustion, and natural state were designed to simulate future change of ecological security. The simulation runs demonstrate that the sustainable development model accords with the patterns of social development. The ecological security levels of natural state model and resource exhaustion model in Chongqing Three Gorges Reservoir are very worrying, since economic losses and environmental impact are severe. But the ecological security level of sustainable development model is relatively good. Net-GDP shows a clear upward trend; the amount of environmental pollution is small. Thirdly, according to the simulation results, ecological security thresholds were got. The thresholds can basically represent the main features of Three Gorges Reservoir's ecological security before 2050. The verification results can be got with the observation of "Net GDP-GDP" values. The overall verification results are appropriate. Then, the status quo of ecological security indicators (2007) was standardized using the determined thresholds. It turns out that the existing 11 indicators are uneven and the overall level is not high. These thresholds were applied into the assessment indices of ecological security for obtaining the comprehensive score of ecological security from 2001 to 2007. The results illustrate that the ecological security in the reservoir area has been emerging an increasing trend, but still in a relatively sensitive period. Consequently, to achieve the sustainable development of the reservoir area requires the cooperation of relevant departments. Finally, on the basis of system dynamics model, the paper determined ecological security index thresholds. Within the range of thresholds, the ecological security can effectively achieve its sustainable development.