Colorectal cancer (CRC) is one of the most common cancers in the world, having both high prevalence and mortality. It is usually diagnosed at advanced stages due to the limitations of current screening methods used in the clinic. There is an urgent need to develop new biomarkers and modalities to detect, diagnose, and monitor the disease. Metabonomics, an approach that involves the comprehensive profiling of the full complement of endogenous metabolites in a biological system, has demonstrated its great potential for use in the early diagnosis and personalized treatment of various cancers including CRC. By applying advanced analytical techniques and bioinformatics tools, the metabolome is mined for biomarkers that are associated with carcinogenesis and prognosis. This review provides an overview of the metabonomics workflow and studies, with a focus on recent advances and findings in biomarker discovery for the early diagnosis and prognosis of CRC.