Ecological security is important in human health, natural resources, and socio-economical development. How to develop an early-warning system is the key problem in ecological security research. Ecological security warning needs to establish the early warning indicator system to reflect the ecological status and development trend. First, in the perspective of identifying factors that affect the eco-system security, the “State-Danger-Immune” (SDI) model is used as a concept model of early-warning indicators. Second, the matter-element model is used on the Formal Description of level of security and early warning objects to establish safety standards and related early warning. The integrated multi-index early warning model can be used to indicate the security state of ecosystems. According to multi-level, multi-dimension and dynamic features of regional ecological security early-warning, the matter-element model is established to assess the regional environmental safety. As a case study, the model is employed to quantitatively assess the ecological security situation of Shaanxi Province from 1990 to 2007. The calculation results show that the ecological environment has shifted from “unsafe” to “relatively unsafe” to “relatively safe” states, which demonstrated that the overall status of ecological security in the Province is undergoing increasing improvement, and the basic ecological destruction can be controlled effectively. However, on the holistic level of ecological security, the safety level of the whole Province is still not satisfactory, because all safety states are less than the general requirement of “Safe”. The results are fundamentally consistent with current real situation. The model carries out the early-warning for ecological security in 2010. The results show that the ecological environment state of Shaanxi Province experienced a gradual improving process from “unsafe”, “relatively unsafe” to “relatively safe” from 1990 to 2007, while its overall level is relatively low; all indicators are below the safety standards. The ecological security will take a “Blue” alert and has the trend of turning into “Yellow” alert of Shaanxi Province in 2010, among which the water resource with an “Orange” alert, which is the main affecting factor to ecological security of Shaanxi Province. In addition, conserving water resources, controlling water pollution, advancing resource utility effectiveness, reducing the impacts of human activities on ecosystems, promoting immunity function of ecological security are necessary for systematically developing and toward a higher level of regional ecological safety. The early-warning model of ecological security, established in this study, has the merits of compatibility and flexibility. Therefore, it can be used not only for specific warning analysis on a particular targeting element of ecological security, but also for transforming multiple-level objective assessment into a single-level objective decision-making to better analyze the regional security status.