The invention belongs to the field of deep processing of starch, and particularly relates to a method for preparing resistant starch employing a microwave technology. The method is characterized by comprising the following steps: (1) preparing a starch emulsion from raw starch, and pregelatinizing the starch by virtue of microwave; (2) carrying out autoclaving treatment on the pregelatinized material at proper temperature and pressure, cooling materials, and hydrolyzing the starch with heat-resistant alpha-amylase and pullulanase until the chain length is 20-120DP; (3) paving the material on a flat plate, storing at 4 DEG C for 3-5 hours, heating the material to 30-50 DEG C by virtue of the microwave, cooling to a room temperature, repeating the temperature circulating process for 2-4 times until the moisture content of the starch is smaller than 14%, crushing and sieving to obtain resistant starch A; and (4) adding water to the resistant starch A, carrying out thermal treatment, adjusting the pH to be 1.5-2, carrying out oscillating reaction, adjusting the pH to be 7-8, adding pancreatin for enzymolysis, filtering and drying a filter cake by airflow until the moisture content is smaller than 14%, and crushing and sieving through a 100-mesh sieve, so as to obtain high-purity resistant starch B.