Canna starch was annealed at sub-gelatinization temperature (50°C) with different annealing time. Small angle X-ray scattering (SAXS) was used to estimate the ultrastructure of the annealed starches with the combined two-phase lamellar model and one-dimensional correlation function. The results showed that, upon annealing, water preferably swelled the amorphous regions of canna starch granules while maintained the part of crystalline region, resulted in an increase in amorphous thickness (da) and lamellar repeat distance (d). Power law plots indicates that a mass fractal (self-similar) structure was observed in canna starch, and annealing induces a less compact structure compared to native canna starch (NCS). Correlation analysis showed that no correlation was existed between annealing time and lamellar peak area, width of peak, and volume crystallinity. However, due to the initial degradation of the amorphous region, the volume crystallinity increased significantly with the increase of crystalline thickness (dc).