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In order to better control the quality of extruded products and to further bridge the gap between extrusion conditions and physicochemical properties of fortified blended food (FBF) from the molecular level, corn soy binary blends (CSB) were produced using single & twin screw extruder (pilot scale) under various extrusion conditions (screw speed, in barrel moisture and feeding rate, specific mechanical energy SME). The physicochemical properties of CSB binary blends including pasting properties, water absorption index (WAI) & water soluble index (WSI), Bostwick flow (BF), and degree of starch gelatinization (DG) were investigated. Results indicated that over 93% of the starch was gelatinized for all the extruded CSB samples. Samples with higher SME showed higher WSI. This was due to the breakdown of the macromolecule which has been confirmed by HPSEC. The WAI showed an increasing trend at initial stage due to the breakdown of starch granule while decreasing when WSI reached a specific value because of the cleavage of both amylose and amylopectin molecule with the increase of SME. BF, which measures consistency and flow rate of FBF porridge, is affected mainly by gelling properties of polymer (mainly starch) in CSB instead of viscosity. Compared to the non-extruded raw material, BF of extruded CSB was significantly increased (p<0.05). Moreover, extruded Sorghum-cowpea (SCB as the positive control) binary blend showed much higher BF when compared to CSB, which was caused by the lower starch molecular weight. All in all, this research developed relationships between molecules & physicochemical properties and extrusion conditions of CSB, which provided theoretical support for the quality control and value added application of extruded FBF.