Porous starch granules (PSGs) are promising biomaterials for the encapsulation, protection, and delivery of bioactive ingredients. In this study, a lipase treatment was first used to generate pores in native starch granules, and then α-amylase was used to enlarge these pores. Electron and fluorescence microscopy analysis showed that the lipase treatment exposed the starch molecules located below the lipid-rich regions on the starch granule surfaces, which increased the swelling of the granules in aqueous solutions. Moreover, lipase treatment caused the surrounding areas to become more loosely packed, which facilitated subsequent starch hydrolysis and the formation of large internal cavities. Fourier transform infrared spectroscopy, X-ray diffraction, and thermogravimetric analyses provided further insights, these methods showed that the short-range order, long-range order, and thermal stability of the PSGs was enhanced by the sequential lipase-amylase modification. PSGs were highly resistant to amylase digestion and had strong adsorption capacity to hydrophobic and hydrophilic substances. This study shows that a combined lipase-amylase treatment can be used to fabricate PSGs, which may have health benefits due to their low digestibility and ability to encapsulate bioactive agents. These PSGs may therefore be suitable for application in the functional food, supplement, personal care, and pharmaceutical industries.