Colorectal carcinoma (CRC) is the third most commonly encountered cancer and fourth cause of cancer-associated death worldwide. Abundant studies have demonstrated that one of the best effective therapies for enhancing the 5-year survival rate of patients is to diagnose the disease at an early stage. Urine metabonomics is widely being utilized as an efficient platform to investigate the metabolic changes and discover the potential biomarkers of malignant diseases. In this study both ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and online affinity solid phase extraction-high performance liquid chromatography (SPE-HPLC) were used to analyze the urinary metabolites from 34 healthy volunteers, 34 benign colorectal tumor and 50 colorectal carcinoma patients to produce comprehensive metabolic profiling data. A reliable separation between the control and disease groups as well as significantly changed metabolites were obtained from orthogonal signal correction partial least squares models which were built based on the two separate data sets from UPLC-MS and affinity SPE-HPLC, respectively. 15 metabolites, showing the metabolic disorders of CRC, were identified finally. These metabolites were found to be related to glutamine metabolism, fatty acid oxidation, nucleotide biosynthesis and protein metabolism.