The Fourier transform infrared spectroscopy and two dimensional correlation analysis method were applied to study a denaturing process of uncross-linked collagen and cross-linked collagen during varying temperature. It was found that the intensity of typically characteristic absorptions of collagen decreased and its peak shifted to low frequency, The amide II central absorbance peak moved to a lower frequency by about ~10 cm-1, which indicated that the inter-chain hydrogen bonds which stabilized the triple helix conformation of collagen were disrupted during thermal denaturation, resulting in a conformational change. The intensity of auto-peak at 1 515 cm-1 was maximum, which suggested that the temperature had a big impact on amide II. In comparison with uncross-linked collagen, the intensity of cross-peaks of cross-linked collagen was weaker, which demonstrated that the effect of temperature on the structure of cross-linked collagen was smaller, and the thermal stability properties of collagen solution could be improved by cross-linking. While the order of second structure changes of cross-linked collagen was different. These fundamental data should provide available information for understanding the relationship between the structure and function of cross-linked collagen.