Micro level characteristics of two different structure stearic acid complexes with high-amylose maize starch were studied. TypeⅠcomplex and type Ⅱcomplex were formed at different crystallization temperature. Better thermal stability was shown on type Ⅱcomplex; the two different complexes both showed V-type crystalline structure,but degree of crystallinity of typeⅠcomplex was higher than type Ⅱ; type Ⅱcomplex appears to be smoother and more homogeneous than typeⅠ on the microscopic level. It revealed that mechanism and interaction of the complexation between amylose and fatty acid were different.