Gastrodia elata has been a valuable medicinal resource in the East for approximately 3000 years. In South Korea, G. elata is cultivated in open-fields or greenhouses near residential areas. However, due to severe continuous damage, cultivation sites need to be frequently relocated, leading to a shortage of available cultivation areas. Alternatively, farmers are focusing on mountain cultivation. This study analyzed suitable cultivation sites for G. elata in mountainous areas using a geographic information system (GIS) and applied various classification methods to identify their characteristics and similarities. The analysis showed that the Natural Breaks (Jenks) classification method maximized the differences between grades, whereas the Quantile method reclassified the area of suitable sites to a relatively high proportion. In contrast, the Equal Interval method reclassified the areas of suitable and unsuitable sites to a lower proportion, whereas the Geometric Interval method best demonstrated extreme-temperature regions as unsuitable sites. Among the classification methods, the Natural Breaks (Jenks) and Geometric Interval methods yielded the most similar results. These findings provide critical methodological outcomes for G. elata cultivation and sustainable agriculture and forestry. Future empirical research and the application of climate change scenarios are necessary to enhance the sustainability of the G. elata cultivation industry.