Arenga pinnata starch (APS) is separated into large and small size fractions. The large granules (APS-L) show a more elongated oval shape, while the small granules (APS-S) are roughly close to a round shape. The large and small granules exhibit a Maltese cross at one end of the APS granules. Both large and small fractions show C-type crystallinity, but the APS-L display a higher crystallinity and more ordered molecular structure. In addition, APS-L have higher helices content than that of APS-S. The APS-L have higher peak viscosity, trough, and final viscosity values, breakdown value, gelatinization enthalpy, and gelatinization temperatures than that of the APS-S, but the APS-L fraction displays a lower setback value. The APS-S gel is more elastic and more solid than APS-L gel. The results indicate that granule size is significantly related to pasting, rheological, and thermal properties of the APS.