We have studied the structure and growth process of hexanethiolate self-assembled monolayers (SAMs) on Cu(100) by means of scanning tunneling rnicroscopy (STM) and X-ray absorption fine structure (XAFS) spectroscopy. At saturated coverage, the thiolates are assembled into a c(2 x 6) structure with zigzag chains along the close-packed Cu rows. The sulfur atom of the thiolate occupies the 4-fold hollow site of the unreconstructed Cu(100) surface with a nearest-neighbor S-S distance of 3.6 Angstrom. Such Sulfur adsorption results in a large lattice mismatch between the S/Cu layer and the alkyl chain layer, since the interchain distance of the alkyl group is ca. 4.5 Angstrom. However, it is reconciled by the internal degree of freedom for the S-C bond,which bridges the two layers, as is confirmed by the geometrical optimization based on molecular force-field calculations. The SAM film formation is well-described by a two-step process: in die first step, a full-coverage monolayer is rapidly formed, which is characterized by a highly oriented but two-dimensionally disordered structure, followed by a much slower evolution to the c(2 x 6) structure with surface diffusion of the thiolate.