Adverse changes of the landscape resulting from diverse human activities have consequently caused quality decline and functional degradation of the natural landscape, endangering the natural habitats of various species. Meanwhile, technical advancements in the area of spatial analysis including GIS and remote sensing enable many kinds of easy-to-quantify landscape indices. Although some systems were developed to support assess landscape indices, developing systems for practical decision-making in spatial planning was insufficient. In this study, the GIS-based Green Infrastructure Assessment System (GIAS) was developed for integrated assessment of diverse landscape ecological values to use in spatial planning and management based upon indices sets that are mainly represented as structure, function, and dynamics of the landscape. In order to verify the effectiveness of the system, two case studies involving the city of Namyangju, northeast of Seoul, were conducted by applying GIAS to the (1) macro scale and (2) micro scale. The study results demonstrate the capability of GIAS as a planning support tool to perform concrete assessment of landscape ecological values and performance both on the macro and micro scale, and its applicability to diverse stages in spatial planning. By utilizing GIAS, frequent human-induced impacts resulting from development projects can be examined in advance, and proactive alternatives can be prepared. In addition, effective decision-making for scientific and systematic planning and management of green infrastructure can be achieved.