This study investigates camel milk protein structural dynamics during digestion using Fourier Transform Infrared (FTIR) spectroscopy and Two-Dimensional Infrared (2D-IR) homo-correlation and hetero-correlation analysis. The synchronous 2DIR homo-correlation map reveals that NH bending and C-N stretching vibrations (amide II) are sensitive to digestion, indicating significant impacts on secondary structures. The asynchronous 2DIR homo-correlation indicates a stepwise process, where initial disruptions in NH interactions precede changes in CO stretching vibrations (amide I), highlighting the sequence of structural alterations during protein unfolding and degradation. 2DIR hetero-correlation spectroscopy, which examines the correlations between amide A (NH stretching vibrations) and amide I, II, and III bands, offers deeper insights into hydrogen bonding dynamics and its influence on protein conformation. This approach elucidates hydrogen bond dynamics by correlating the fast-changing NH stretching vibrations with the slower amide band vibrations, hetero-correlation reveals how initial hydrogen bond disruptions lead to broader structural changes in the protein backbone. It also elucidates the conformational stability and flexibility by indicating how variations in hydrogen bond intensity correlate with the strength and flexibility of different secondary structural elements, providing a nuanced understanding of the protein's behavior during digestion. These findings indicate the potential of FTIR combined with 2D-IR for monitoring digestive processes.