Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy using a special waveguide based on a silver halide fiber was used for probing the heat-induced secondary structure and conformation changes of bovine serum albumin (BSA). From the secondary derivative and the curve fitting of the obtained ATR-FTIR spectra, the changes of the BSA secondary structure with temperature were clearly identified. Two different thermal denaturation temperature ranges (i.e., 50–52 and 80–82 °C, at which a change of the protein structure occurred) were determined, while only one denaturation temperature was previously identified via classical FTIR measurements. Additionally, taking advantage of two-dimensional correlation spectroscopy more detailed information on changes of the protein secondary structure was revealed. The developed method facilitates in situ, sensitive, and more in-depth probing of protein secondary structures, which represents a significant advancement compared to conventional characterization methods.