An optimal slowly digestible starch (SDS) content was obtained through assessment of variation in digestibility of pullulanase debranched waxy maize starch which was recrystallized for up to 8 days. The effects of debranching time, debranching enzyme concentration, storage time and temperature on digestibility and structural properties of waxy maize starch samples were investigated. When gelatinized starch was treated with higher enzyme concentration and less debranching time, higher SDS was formed while resistant starch (RS) increased with time. The maximum SDS content was obtained by debranching for 3–6 h with high pullulanase (20 or 40 ASPU/g) then storing at 4 °C for 2 days. X-ray diffraction pattern of treated starch at optimal conditions was similar to the B-type in which illuminated treated starches contain partially ordered crystalline structures. Scanning electron micrographs showed the treated starch had more irregular angular shapes with a higher crystallinity structure and pitted surface as debranching and recrystallization time increased. In differential scanning calorimetry thermograms, the melting temperature and enthalpy of treated starches were gradually enhanced, resulting from reforming of double helix structure by low temperature recrystallization following debranching. These changes suggested that SDS mainly consists of a small portion of partially ordered double helix crystalline components with short amylopectin chains and amorphous components.