Using wheat starch as raw material, and thermostable α-amylase SPEZYME Fred as liquefacient, isomalto-oligosaccharide was prepared. The factors which affected liquefying of wheat starch were investigated by orthogonal tests. The results showed that the optimum condition was as follows: pH value was 5.6～5.8, the mass percent of starch pulp was 25%, liquefying temperature was 85℃, the usage quantity of SPEZYME Fred was 14LU/g, liquefying time was 80 minutes. On this condition, DE value of liquefied solution was 15.62%. The topology nanostructure of starch pulp was researched by atomic force microscopy when the wheat starch was not liquefied and DE value of liquefied starch pulp was 7～9 and 11～13. Image evidence of starch granules' structure change was obtained. With the increase of liquefied degree, Starch granules were broken up gradually and became branch structure. These images proved that starch granules were composed of particle structures, amylose structures and amylopectin structures.