Due to the potential reduction in starch availability, as well as the production of the distinct physico-chemical characteristics of starch in order to improve health benefits, the formation of starch–lipid complexes has attracted significant attention for improving the quantity of resistant starch (RS) content in starchy-based foods. The purpose of this research was to apply ultrasonication to produce intermediate amylose rice (Oryza sativa L.) cv. Noui Khuea (NK) starch–fatty acid (FA) complexes. The effects of ultrasonically synthesized conditions (ultrasonic time, ultrasonic amplitude, FA chain length) on the complexing index (CI) and in vitro digestibility of the starch–FA complex were highlighted. The optimum conditions were 7.5% butyric acid with 20% amplitude for 30 min, as indicated by a high CI and RS contents. The ultrasonically treated starch–butyric complex had the highest RS content of 80.78% with a V-type XRD pattern and an additional FTIR peak at 1709 cm−1. The increase in the water/oil absorption capacity and swelling index were observed in the starch–lipid complex. The pasting viscosity and pasting/melting temperatures were lower than those of native starch, despite the fact that it had a distinct morphological structure with a high proportion of flaky and grooved forms. The complexes were capable of binding bile acid, scavenging the DPPH radical, and stimulating the bifidobacterial proliferation better than native starch, which differed depending on the FA inclusion. Therefore, developing a rice starch–lipid complex can be achieved via ultrasonication.