In this study, we report the first production of two-dimensionally well-ordered molecular multilayers (i.e., with a well-defined molecular lamellar structure) based on the antiparallel beta-sheet chain conformation in thin films of a brush polypeptide, poly(S-n-hexadecyl-DL-homocysteine) (PHHC), through the use of a simple spin-coating process and the quantitative structural and property analysis of the thin films using a grazing incidence X-ray scattering technique combined with Fourier transform infrared spectroscopy and differential scanning calorimetry. These analyses provide detailed information about the structure and molecular conformation of the self-assembled lamellae in the PHHC thin film, which is not easily obtained using conventional techniques. Moreover, we used the in situ measurements carried out at various temperatures and the data analyses to establish mechanisms for the evolution of the self-assembled lamellar structures in the film and for their melting. In addition, we propose molecular structure models of the PHHC polymer molecules in the thin film at various temperatures.