[Objective] To research on the chemical component changes of RADIX ASTRAGALI and RADIX NOTOGINSENG after compatibility by two different extracting methods. [Method] Changes of chemical components in compatibility extracting solution and single drug extracting solution were compared by HPLC. Combined with the molecular weight information provided by LC-MS, structures of the changed chemical components were deduced. [Result] Compared with the ethanol extracting method, water extracting-alcohol precipitating method had significantly higher contents of ginsenoside Rh1 and Rg2; and ginsenoside Rh4 and notoginsenoside T5 and Fe were detected only in the water extracting-alcohol precipitating solution; other 4 chemical component peaks were only detected in the ethanol extracting solution with low polarity, but they were not found in the water extracting-alcohol precipitating solution. [Conclusion] As for the compatibility extracting solution and single drug extracting solution, no new chemical components were detected in the extracting solution before or after compatibility, but the contents of some chemical components enhanced after compatibility. As for the different extracting methods, dissolution types and contents of chemical components changed significantly in compatibility extracting solution, especially the chemical components dissolution of RADIX NOTOGINSENG.