Microwave irradiation is a rapid and efficient method to synthesize oligomers and can be employed in polysaccharides production. As an artificial polysaccharide, polydextrose is known for its solid performance in food processing and its additional health benefits. This study was aimed at producing polydextrose by microwave irradiation using glucose and sorbitol as substrates; water and phosphoric acid as initiator and catalyst. The actual maximum yield was 99%. Synthetic polydextrose were purified by ethanol elution and Sepherdex G-25 column chromatography. Its purity was demonstrated by the high-performance gel-permeation chromatography as a single symmetrical sharp peak, additionally the average molecular weight was calculated to be 2.131 kDa. FT-IR spectra showed that the synthesized polydextrose has the structural feature similar to Polydextrose-Litesse(®). In vitro fermentation revealed that polydextrose possesses the biological function similar to Polydextrose-Litesse(®) in increasing the concentration of short chain fatty acid and decreasing pH. This research demonstrated the feasibility of a rapid and efficient microwave mediated method to synthesize polydextrose and potentially other value added carbohydrate polymers.