The processing of biological raw materials is considered to have an important role in the therapeutic application in Traditional Chinese Medicine. The root of Rehmannia glutinosa has to be processed by nine cycles of rice wine immersing, steaming and drying before using in clinical applications. In order to understand the chemical changes resulting from the processing, a comprehensive analysis of Rehmanniae radix was made using (1)H-NMR and Fourier transform (FT)-mass spectrometry in combination with multivariate data analysis. After (1)H-NMR and principle component analysis, hydrolysis was found to be the major chemical process during the treatments. Catalpol, raffinose and stachyose levels gradually decreased during processing, whereas monosaccharides including galactose and glucose were found to be higher in processed roots. The metabolic profile changed gradually through the processing cycles although the differences became smaller after the fifth processing cycle. The positive and negative ion-mode mass spectra by high resolution FT-MS revealed several series of ion clusters with mass differences of 162.053 Da, indicating a difference of a hexose moiety. During the processing, the number and signal intensity of the smaller glycosides were increased. Therefore, these results indicate that the fresh Rehmanniae radix is rich in polysaccharides, which are hydrolyzed during the processing.