This study was carried out to offer the basic methodology of the system and model to objectively assess the natural ecosystem for environmentally friendly land conservation and present the alternative plan on establishing the environmental policy. The results of this study were as follows. We selected four assessment factors associated with biotic, abiotic, qualitative, and functional factors. Also, there were extracted fifty-six indicators including density, total nitrogen, hemeroby degree, and goods production. The assessment factor showed that biotic one was very important. The importance of indicators were analyzed that rare and endangered plant was important in biotic factor, in case of abiotic, qualitative, and functional factors, organic matter, landscape diversity, and conservation of ecosystem were greatly important. The results of factor analysis on the characteristics of indicators, classified biotic factor into six factors including a structural one, abiotic factor as a soil and physical one, qualitative factor as five ones including hierarchical one, and functional factor as public and conservational one. In the results of analysis on assessment model, R-square of biotic factor was 51.7%, those of abiotic, qualitative, and functional one were each 58.4%, 44.2%, and 39.3%, and statistical problem was no existence. In future, to develop the assessement model and methodology of sustainable natural ecosystem, we will have to achieve the integrated model and grouping by assessment factor.