X-ray photoelectron spectroscopy (XPS) was measured for the dry body of hydroxyapatite (HAP)-collagen (COL) nanocomposites cross-linked using glutaraldehyde (GA). Survey scan XPS showed the elemental spectra of N, C, O, Ca and P, which came from HAP and COL. The covalent bond formation between Ca2+ of HAP and RCOO- of COL molecule was confirmed by XPS. The bridge formation between COL fibers could be assessed from C1s and N1s band spectrum. The dehydration of swelling water during drying led to the reduction of linking distance for pendant GA between COL fibrils and contributed to further cross-linkage reaction. Cross-linkage induced the enlargement of length scale unit of COL. The modification of length scale was doing the key role of structure manipulation in the cross-linked HAP-COL nanocomposites.