Resistant starch (RS) has the advantage of reshaping gut microbiota for human metabolism and health, like glycemic control, weight loss, etc. Among them, RS3 prepared from pure starch is green and safe, but it is hard to achieve structural control. Here, we regulate the crystal structure of starch with different chain-length distributions (CLDs) via extrusion at low/high shearing levels. The change in CLDs in extruded starch was obtained, and their effects on the fine structure (Dm, dBragg, dLorentz, degree of order and double helix, degree of crystal) of RS and its physicochemical properties were investigated by SAXS, FTIR, XRD and 13C NMR analyses. The results showed that the RS content under a 250 r/min extrusion condition was the highest at 61.52%. Furthermore, the crystalline system induced by high amylopectin (amylose ≤ 4.78%) and a small amount of amylose (amylose ≥ 27.97%) was favorable for obtaining a high content of RS3-modified products under the extruding environment. The control of the moderate proportion of the A chains (DP 6-12) in the starch matrix was beneficial to the formation of RS.