Humans can be considered as super-organisms with an internal ecosystem of diverse symbiotic microbiota that have interactive metabolic processes. The homeostatic balance and the metabolome of an organism are then dependent upon not only the host but also the interaction between the host and its microflora complement or co-metabolome. Short chain fatty acids (SCFAs), as end products of the gut microflora-host metabolic interactions, are the principal anions which arise from bacterial fermentation of undigested dietary carbohydrates in the colon. The SCFAs production, absorption and metabolism have presented various profound effects on the host lipid metabolism, energy metabolism, mineral absorption and satiety. The function of maintaining host metabolic homeostasis and colonic health might be attributable to the activation of SCFAs receptors. The SCFAs have currently become the subject of numerous physiologic and clinical studies. However, there is lack of a powerful tool for simultaneous assessment of the changes of the gut microflora and of the SCFAs production and ratio. With the advent of the post-genomic era, metabonomics has been identified as a very promising approach to understand the underlying mechanism occurred between SCFAs, gut microflora and host.