In vitro digestibility and physicochemical properties of chitosan (CS)-modified Arenga pinnata starch (APS) after heat-moisture treatment (HMT) were evaluated. HMT would limit the enzymatic hydrolysis of APS and the digestion rate of HMT-APS-CS was further reduced with the decrease of CS molecular weight. CS and HMT inhibited the solubility (SOL) and swelling power (SP) of APS, and the inhibition effect was more obvious with the decrease in CS molecular weight. Changes in the pasting properties of the CS-modified APS indicated that the initial structure of the APS granules was destroyed with the formation of a denser structure. The increase of the relative crystallinity and the aggregation of the APS granules were related to starch cross-linking confirmed by Fourier transform infrared. The interactions between CS and APS granules after HMT greatly altered granular morphology and internal structure of APS. Therefore, the improvements of SDS and RS of HMT-APS-CS were mainly related to CS covering the surface of the APS granules, granule aggregation and HMT-induced changes in the internal structure of the starch granule.