The preparation process of resistant starch III (RS3) has attracted widespread attention, but its milling method is often overlooked. This study examines two milling methods for RS3: shear milling (SM) and vibration milling (VM). Manual milling (MM) is used as a control. The particle size, morphology, crystallinity, gelatinization characteristics, and in vitro digestibility of milled RS3 are analyzed. The particle size of the VM‐samples ranged from 71.92 to 107.69 µm, which is lower than SM‐samples. Scanning electron microscopy shows that SM‐RS3 appears as pellets, while VM‐RS3 is mostly coarse flakes. From the results of RVA and DSC, VM destroys more starch than SM. The crystallization peak of VM‐samples disappears, and the retention of SM‐samples is well. The values of R 1047/1022 and R 995/1022 cm−1 indicate that the crystal order and double helix structure of RS3 are destroyed after multiple VM shocked compared with SM. In vitro digestion experiment, resistant starch content of SM‐samples is about 30%, while VM‐samples are much less than SM. These findings suggest that the choice of milling methods has a significant impact on the structure and physicochemical characteristics of RS3, and it is an important step in preparing RS3.