Objective To investigate the effects of pullulanase treatment on the structure and functionality of waxy corn starch, providing theoretical guidance for regulating starch debranching modification.Methods The effects of pullulanase treatment on the structure and functional properties of waxy corn starch are systematically studied using scanning electron microscopy, X-ray diffraction, relative molecular weight and distribution, apparent amylose content, and digestibility tests.Results Compared with untreated starch, after pullulanase treatment, starch solutions of different mass fraction rearrange to form a relatively ordered aggregated structure containing B-type crystallinity, with the relative crystallinity increasing from 2.70% to 22.67%. The resistant starch content increases from 12.41% to 39.25%.Conclusion Pullulanase treatment significantly affects the structure and functional properties of waxy corn starch. After pullulanase treatment, starch in high mass fraction solutions is more likely to aggregate and rearrange into ordered aggregates during the enzymatic process compared to starch in low mass fraction solutions. This delays the catalytic effect of pullulanase on starch, resulting in high molecular weight starch in high mass fraction solutions.