The invention relates to the technical field of modified starch and particularly discloses a method for preparing the starch fatty acid ester through a mechanical activation-microwave solid phase method. The method comprises the following steps: uniformly mixing the starch and the fatty acid according to a certain proportion, adding into a ball mill to mechanically activate, dipping a catalyst to synchronously perform a first esterification reaction to obtain the primary starch ester, taking out and adjusting the water content, performing microwave heating to perform a secondary esterification reaction to obtain the starch ester with a high substituted degree, rinsing by ethyl alcohol and baking to obtain the starch fatty acid ester. By adopting the preparation method, the starch and the fatty acid are subjected to two esterification reactions, and the product starch ester is high in substituted degree and excellent in performance. The method is simple in process, mild in reaction condition, easy in operation, free of environment pollution and low in cost, and is suitable for industrial production.