Potato starch (PS) is widely used in the food industry, but its uncontrolled paste consistency and poor film properties greatly limit its utilization. To expand its application, PS is separated into small- (PS-S), medium- (PS-M), and large- (PS-L) fractions and modified by “high-pressure microfluidization” (HPM). The effect of HPM on the microstructure, physicochemical properties, and digestibility of fractionated PS is investigated. Results show that the mechanical forces produced by HPM_{(50–150 MPa)} can break PS molecules and enhance digestion rate with increasing pressure. Meanwhile, the relative crystallinity (RC) of HPM_(150 MPa)-modified PS-L, PS-M, and PS-S decreases by about 29.23%, 15.40%, and 9.33%, respectively, relative to the RC of native fractionated PS. The changes in 1047/1022 and ΔH values in the three fractions show similar trends. Thus, the changes in microstructure of HPM-modified PS-L show more considerable than that of PS-S. Compared with the native ones, the final viscosity of HPM_(150 MPa)-modified PS-L, PS-M, and PS-S decreases by about 61.86%, 41.61%, and 35.70%, respectively, and the setback value increases to 379.67, 479.67, and 493.00 cp, respectively. These results indicate that HPM-modified PS-S has a higher tendency to form edible films than PS-L. Therefore, HPM-modification may expand the industrial application of fractionated PS.