In the current study, the effects of extrusion using a haake rheometer with a twin-roll mixer, with and without FA addition, on the structures and in vitro digestibility of starches from different sources were investigated. After extruding for 15 min at 90 °C with a moisture content of 40 %, no matter FA was added or not, lager Ap molecules were preferentially debranched, while Am with longer CL were depolymerized simultaneously, resulting to reduced averaged molecular size of Ap and shortened Am chains. Of all starches, regardless of their botanical backgrounds, although synergic effects were found between extrusion and FA addition on reducing their relative crystallinity and the ordered structures, distinctly different effects on the in vitro digestibility of these starches have also been observed especially regarding the digestion of starch branches with DP > 10 Particularly, the Am chains with DP 10-1000 was remaining undigested when FA was added. This study provides important information concerning how to adjust starch digestibility into a healthy range through altering the starch structures using extrusion technique with the addition of phytochemicals or not.