Colorectal cancer (CRC) is mainly depended on the radical operation, the changing energy metabolism after operation reflects the extent, the magnitude, and the degree of surgical trauma. The aim of this study was to analyse the biochemical perturbation in the serum of CRC after operation and to evaluate their involvement in the progression of CRC. Gas chromatograph-mass spectrometry (GC-MS) in combination with pattern recognition techniques (Partial least squares discriminant analysis, supervised clustering analysis) was used to analyze serum metabolome in 30 CRC patients. A 34 endogenous metabolites included amino acid, fatty acid, carbohydrate and other intermediate metabolites were identified. Partial least squares discriminant analysis based on these metabolites discriminated preoperative from postoperative CRC group. Compared with preoperative CRC patients group, decreases in L-valine, 5-oxo-L-proline, 1-Deoxyglucose, D-turanose, D-maltose, arachidonic acid and hexadecanoic acid levels and increases in L-tyrosine levels were observed in postoperative CRC patients group. The result demonstrated the GC-MS technique is an valuable tool for the characterization of the metabolic perturbation, and the metabolomic study will certainly benefit for monitoring the nutrition state of CRC patients, the prognosis and therapy evaluation of CRC patients after operation.