We investigate surface morphology and crystalline structure of biodegradable polymers poly(3-hydroxybutyrate) (PHB) and its random copolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(HB-co-HHx), HHx = 12 mot %) using surface-sensitive techniques. Surface region typically to a depth of about 10 nm of polymer films which have thickness ranging from 20 to 120 nm is observed by grazing incidence X-ray diffraction (GIXD), X-ray reflectivity (XR), and atomic force microscopy (AFM). Both PHB and P(HB-co-HHx) show that crystallographic b-axis of crystallites in the surface region is aligned in the direction normal to the surface. It indicates that intermolecular interaction along a-axis is still dominant in the surface region, which would also determine the fastest growth direction of crystalline lamellae. A lattice relaxation peculiar to P(HB-co-HHx) surfaces is recognized in the b-axis length. As temperature is raised, crystalline lamellae characterized by densely packed molecular chains appear, implying a thermally activated transformation from metastable lamellae to stable ones. The metastable lamellae in which molecular chains fold loosely are mainly observed throughout rapid cooling, although the loosely and densely packed lamellae equally form in slow cooling. Furthermore, continuous lamellae melting at the surface is observed, all of which suggest an additional process for forming the metastable long-range order in the surface region. Crystallinity at polymer surface would also be responsible for the difference in surface morphology between PHB and P(HB-co-HHx) revealed by XR and AFM.