The thermal stability of collagen has an important effect on its practical applications. Many believe that hydroxyproline (Hyp) improves the structural stability of collagen molecules. In this study, for the first time, a method of building natural collagen molecular models was described. We constructed a collagen model with typical triple-helix structure and calculated the hydrogen bond energy between collagen alpha chains. The calculated hydrogen bond energy was consistent with the experimental results of differential scanning calorimetry. After the calculation simulation, we verified that the hydrogen bond energy between collagen chains was positively correlated with Hyp content in the models and an increased Hyp content in the model was beneficial in improving the thermal resistance of the structure. In addition, we found that thermal unfolding did not occur simultaneously along the entire molecule but started in the regions with less Hyp content. This study provides a collagen model with a natural collagen amino acid further investigation of the physical and chemical properties of natural collagen. sequence, I which will be helpful for