Microwave (MW) heating shows higher efficiency in preparing wheat starch-stearic acid (WS-SA) complexes than the traditional water bath (WB) heating method, while the detailed "time-energy-quality" evaluations and the potential anti-digestion mechanism of the MW-processed WS-SA remain further exploration. In this study, 95 % time cost and 73 % energy consumption were saved when using MW processing WS-SA, and the MW-processed complexes were verified to show significantly higher relative crystallinity, short-range ordered structure degree, thermal stability, complex index, and resistant starch content. Molecular dynamics (MD) simulation demonstrated that MW treatment notably facilitated the binding rate of amylose and SA molecules, generating a tight and stable helical structure through hydrogen bonds and van der Waals forces. Analyses of solvent-accessible surface area and water status cross-verified that the denser structure could endow the MW-processed complexes with higher resistance to water solvation effects and correspondingly reduce the water mobility for enzymatic hydrolysis reactions, ultimately making the MW-processed complexes more undigestible. This study provides a further understanding of the anti-digestion mechanisms of the MW-processed WS-SA from the molecular level, and it is expected that the current work could attract more concerns to the highly cost-effective MW heating method for processing starchy food.