In order to investigate the effect of thermostable α-amylase on the rice physicochemical properties, free/bound phenolics, and antioxidant capacities during extrusion, seven different gradients of enzyme concentration from 0 to 6 ‰ (db of starch) were used for both hulled and whole rice. For rice treated with the same extrusion conditions, special mechanical energy (SME) input changed slightly in the presence of fiber fraction (bran/husk), while decreased greatly with increasing α-amylase levels due to the reduced viscosity and friction between mechanical elements and materials. Huge physicochemical modifications were achieved in expansion ratio (ER), bulk density (BD), water absorption/solubility indices (WAI/WSI), and viscosity via enzymatic liquefaction. The total phenolic content (TPC) retention increased dramatically (93.06 and 86.33 % for hulled and whole rice, respectively) with increasing enzyme concentrations to 6 ‰, indicating that a milder reaction environment was created with less thermal-mechanical impact on phenolics. By linear analysis, the TPC of extruded rice hulled or not was strongly and positively related with BD (R = 0.9185 or 0.9719) and WSI (R = 0.9719 or 0.8857), whereas negatively related with SME (R = −0.9460 or −0.8906). Besides, the free/bound phenolics combined with antioxidant activities (1,1-diphenyl-2-picryl-hydrazyl (DPPH), 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid (ABTS), and ferric reducing antioxidant power (FRAP)) were all improved significantly by the separate/synergetic addition of enzyme and bran/husk used as, respectively, the “special protective agent” and rich source of bioactive compounds. In summary, thermostable α-amylase could achieve many beneficial effects on both physicochemical properties and antioxidant activities of rice extruded with/without fiber for promoting the development of cake making, wine brewing, infant food industries, or animal husbandry.