Synbiotics refer to biological agents (probiotics) used in combination with probiotics. In recent years, accumulating studies have reported that synbiotics possess many health benefits. The efficacy of symbiotics is affected by the selection of probiotics and prebiotics. Fructooligosaccharides and inulin are commonly used as probiotics, which can be selectively absorbed by probiotics in the intestine and promote the proliferation of probiotics, thereby keeping the host healthy. This paper reviews the differential metabolism and metabolism pathways of fructooligosaccharides (FOS) and inulin by lactic acid bacteria, and summarizes the mechanisms of action of the hydrolases, transport systems, and regulatory proteins at the molecular level in order to provide basis for understanding the regulatory mechanism of the metabolic network of FOS and inulin by lactic acid bacteria. Besides, it summarizes the recent applications of synbiotics containing FOS and/or inulin with a view to providing valuable evidence to extend the combined application of prebiotics and probiotics.