The characteristics of decoction water are important for the extraction of herbal drugs. In this study, the relationship between the characteristics of water and extraction efficiency of bioactive compounds from Corydalis tuber was investigated. Six different types of decoction water, including three types of mineral water from Jeju Island and three types of bottled water sold in market, were used as decoction water for the extraction of bioactive compounds from Corydalis tuber. The contents of minerals in six types of water were analyzed by ICP-AES and ICP-MS; the contents of extracted bioactive compounds were analyzed by HPLC. Multivariate analysis of variance was used to analyze the differences in total extraction and bioactive compounds extracted with six types of water. Multiple factor analysis was used to analyze the relationship among the pH, content of mineral, anion, total extractions and content of bioactive components as factors. There was a significant difference among the six types of water in the total extracts and the bioactive compounds. The results proved that the content of extracted compounds from Corydalis tuber was influenced by the types of decoction water.