Ecological integrity is the capability to support and maintain a balanced, integrative and adaptive biologic system, having the full range of elements and processes expected in the natural habitats of a region. Assessment of ecological integrity has great significance for preventing sensitive nature habitats from human disturbance. The theory of dissipative structures suggests that the stressors from human activities, as well as the biological, physical and chemical integrity and ecosystem function that reflect the ability of self-organizing, can well indicate the integrity of an ecosystem. This paper summarized the experiential indicators for assessing the integrity of aquatic and terrestrial ecosystems and the stressors from human disturbance, and discussed the methods for selecting priority indicators and comprehensive assessment in actual assessment programs. The prospects of further study were discussed, according to some issues existed in published researches.