Understanding the thermal stability of the proteins in human serum is essential since human serum is the important source of pharmaceutical proteins. Near-infrared(NIR) spectroscopy was applied to the investigation of thermal changes in secondary structure and hydration of human serum proteins.However, as a multicomponent system, the overlap of the broad NIR bands makes the structural analysis very difficult directly using the spectra of serum samples. Therefore, continuous wavelet transform(CWT) was used to improve the resolution of NIR spectra, and Monte Carlo-uninformative variable elimination(MC-UVE) method was applied to the selection of the variables associated with the proteins for the structural analysis. The variables(5956, 5867, 5815, 5747, 4525, 4401, 4359 and 4328 cm~(-1)) related to protein secondary structures and those(7074, 6951, 6827 and 6700 cm 1) connected with water species were selected. Then, the thermal stability was analyzed through the intensity variations of the selected variables with temperature from 30 C to 80 C. It was found that the variation of the spectral variables related to both a-helix and b-sheet changes apparently around 60 C, indicating the beginning of the thermal denaturation and the transition from a-helix to b-sheet. Moreover, an obvious change was found around 60 C for the content of the water specie S_3, i.e., the water cluster containing three hydrogen bonds. The result demonstrates that MC-UVE can identify the protein-related NIR spectral variables, and the water species may be a marker for investigation of the structural change of proteins in biochemical systems. Understanding the thermal stability of the proteins in human serum is essential to human serum is the important source of pharmaceutical proteins. Near-infrared (NIR) spectroscopy was applied to the investigation of thermal changes in secondary structures and hydration of human serum proteins. However, as a multicomponent system, the overlap of the broad NIR bands makes the structural analysis very difficult directly using the spectra of serum samples. Thus, continuous wavelet transform (CWT) was used to improve the resolution of NIR spectra, and Monte Carlo-uninformative variables elimination (MC-UVE) method was applied to the selection of the variables associated with the proteins for the structural analysis. The variables (5956, 5867, 5815, 5747, 4525, 4401, 4359 and 4328 cm -1) related to protein secondary structures and those (7074, 6951, 6827 and 6700 cm 1) connected with water species were selected. Then, the thermal stability was analyzed through the intensity variations of t he selected variables with temperature from 30 C to 80 C. It was found that the variation of the spectral variables related to both a-helix and b-sheet changes apparently around 60 C, indicating the beginning of the thermal denaturation and the transition from a -helix to b-sheet. Moreover, an obvious change was found around 60 C for the content of the water specie S_3, ie, the water cluster containing three hydrogen bonds. The result demonstrates that MC-UVE can identify the protein-related NIR spectral variables, and the water species may be a marker for investigation of the structural change of proteins in biochemical systems.