To study the effects of cooking methods on the structure and digestion changes of starch encapsulated by cellular structure, intact potato parenchyma cells were successfully isolated and then subjected to different domestic cooking methods, including baking, frying, boiling, and autoclaving. The morphology, crystalline structure, thermal properties, and in vitro starch digestibility of cooked cell samples were investigated. Our results indicated that potato cell walls remained intact and performed as physical barriers preventing the diffusion/absorption of α-amylase to intracellular starch substrates after baking or frying treatment. However, boiling or autoclaving treatment destroyed cell wall structure, and the disrupted cellular structure reduced the digestion rate, likely by inhibiting diffusion of amylase through a weakened cell wall barrier, but could not lower the final digestion extent when compared to the pure starch. These findings suggested that potato products with lower glycemic index can be obtained by baking or frying treatment.