According to the characteristics of the regional composite eco-system, the system dynamics model of Chongming’s regional eco-security is constructed on the basis of the five subsystems of economy, population, resources, environment, ecology as well as 71 parameters. With net GDP as the reference we used situation simulation and a trend analysis of the eco-security was conducted to determine the eco-security threshold. The eco-security threshold value indicates the turning point in the change of ecological quality and can help determine ecosystem health and safety as well as function as a control threshold for all constructions in the process of regional construction and development. System simulation was used to verify this threshold value. We discovered that the threshold was the frame of reference of eco-security characteristics under certain a developmental mode and reflected the dynamic developmental trend of the system. The paper overcomes the static nature of current eco-security threshold research. Furthermore, the threshold was applied in eco-security assessment and factor analysis. We found that the comprehensive score of eco-security of Chongming increased in recent years due to the orientation of “ecological island” and the implementation of ecology guarantee measures. In 2007 the comprehensive score for the eco-security of Chongming was 0.523 and still remains at a medium level. A factor test using the threshold value as the standard showed a large difference between the major security factors. The major limiting factors include environmental pollution and energy use.