The objective of this study is to propose a method for computing the Natural Drought Index (NDI) that does not consider man-made drought facilities. Principal Component Analysis (PCA) was used to estimate the NDI. Three monthly moving cumulative runoff, soil moisture and precipitation were selected as input data of the NDI during 1977∼2012. Observed precipitation data was collected from KMA ASOS (Korea Meteorological Association Automatic Synoptic Observation System), while model-driven runoff and soil moisture from Variable Infiltration Capacity Model (VIC Model) were used. Time series analysis, drought characteristic analysis and spatial analysis were used to assess the utilization of NDI and compare with existing SPI, SRI and SSI. The NDI precisely reflected onset and termination of past drought events with mean absolute error of 0.85 in time series analysis. It explained well duration and inter-arrival time with 1.3 and 1.0 respectively in drought characteristic analysis. Also, the NDI reflected regional drought condition well in spatial analysis. The accuracy rank of drought onset, termination, duration and inter-arrival time was calculated by using NDI, SPI, SRI and SSI. The result showed that NDI is more precise than the others. The NDI overcomes the limitation of univariate drought indices and can be useful for drought analysis as representative measure of different types of drought such as meteorological, hydrological and agricultural droughts.