•The structure of waxy maize starch during debranching was investigated.•Pullulanase was able to debranch more than 80% waxy maize starch.•Resistant starch content of debranched waxy maize starch was greater than 60%. Pullulanase is able to debranch amylopectin and result in higher resistant starch (RS) content in waxy maize starch. Different levels of pullulanase have been used to debranch waxy maize starch in the literature, but the changes of structure during debranching are unknown. In this study, waxy maize starch (25% solids) was cooked and debranched with different levels of pullulanase. The structure of waxy maize starch during debranching was investigated and the digestibility of the debranched products was measured. When pullulanase activity was increased, more amylopectin was debranched in same debranching time, and the degree of crystallinity and the RS content were increased. With longer debranching time, more linear chains were cleaved and crystallized to B-type crystalline structure at 25 °C. More than 80% of waxy maize starch could be debranched by pullulanase. After the debranched starches were crystallized at 25 °C for 24 h, the RS content was increased to 70.7%.