Thin films of poly(L-lactide) (PLLA)/atactic poly(3-hydroxybutyrate) (ataPHB) blends with different miscibility were prepared and characterized by using differential scanning calorimetry (DSC) and atomic force microscopy (AFM). The DSC analysis suggested that the blend thin films exhibited different phase structures, such as miscible, partially miscible, and immiscible depending on the blending ratio as well as molecular weight of ataPHB component. The different miscibility was further confirmed by the surface morphological observation by AFM. Both the immiscible and partially miscible blends of PLLA/ataPHB revealed the formation of phase-separated morphology of PLLA and ataPHB components, whereas the homogeneous surface morphology was observed for the miscible blend. On the basis of the changes in the depth profile from the surface level of the thin films, the enzymatic degradation rates of the PLLA and ataPHB domains were determined in the presence of either PHB depolymerase or proteinase K, respectively. The erosion rate of PLLA/ataPHB blends was strongly dependent on the blend composition and the degree of dispersion of the two components. The enzymatic degradation behaviors were discussed in terms of phase structure, molecular mobility, and retardation effect of the components in the blends.