This study investigates the effects of the debranching time of waxy potato starch using pullulanase and recrystallization on particle morphology, debranching degree, and crystal structure. The results demonstrated that after gelatinization and debranching, the surface of the starch crystals became rough and uneven due to hydrolysis, with most particles showing a fragmented surface. The crystalline state was not significantly changed with debranching time. X-ray diffraction analysis revealed no significant differences in the patterns of recrystallized linear dextrin (LD) after various debranching times. Notably, the short-range ordered structure of LD after debranching and recrystallization was more organized than that of the original or gelatinized starch. Additionally, polarized light microscopy showed that the birefringent pattern disappeared as a result of debranching and recrystallization, indicating the breakdown of particle structure, although the overall particle morphology did not change significantly with varying debranching times. Furthermore, linear dextrin derived from starch debranched for 6 h (with pullulanase at 15 μg/g) successfully embedded stearic acid, oleic acid, and linoleic acid, forming a VI-type starch–fatty acid complex.