Cordyceps is a famous traditional Chinese medicine (TCM) that has been used in China for hundreds of years.In the present study a multi-column liquid chromatography (MC-LC) system was developed for the qualitative analysis of macromolecules and micromolecules in Cordyceps.The MC-LC system includes a size exclusion pre-column,a size exclusion column (SEC) and a reversed phase column (RP) which were controlled by column-switching valves.The sample was separated by the size exclusion pre-column into two fractions (macromolecules and micromolecules).These fractions were further separated on SEC and RP columns,respectively.A diode array detector (DAD) and a mass spectrometer (MS) were used to detect the components.This MC-LC method was utilized for analysis of Cordyceps samples.Two macromolecular peaks and 15 micromolecular peaks were found in Cordyceps,and 11 of the micromolecular peaks were identified as adenosine-5'-monophosphate (AMP),phenylalanine,uridine,hypoxanthine,inosine,guanine,guanosine,deoxyadenosine-5'-monophosphate (dAMP),adenosine,adenine and cordycepin (or its isomer).This method is useful for quality control of Cordyceps.