The present study systematically investigated the effects of alcohols, including methanol, ethanol, n-butanol, and propanol with different hydroxyl group numbers and locations on the thermal stability and molecular aggregation behavior of collagen. The results of ultra-sensitive differential scanning calorimetry (US-DSC), dynamic light scattering (DLS) and intrinsic fluorescence showed that with the increase of carbon chain length, alcohols can denature collagen, accompanied by transition in triple helical structure, promoted aggregation behavior, and altered molecular interactions. However, with the number of hydroxyl groups in alcohol molecules increased, the thermal stability of collagen increased and the molecules tended to disperse. Furthermore, radial distribution function (RDF) results showed that alcohols can change the structure of the hydration layer around collagen, thus altering the aggregation morphology of collagen molecules in solution. The results of the interaction between components in different alcohol systems demonstrated that with the decrease of alcohol polarity, bridge bond networks were formed between collagen molecules. Specifically, it was found that because the hydroxyl groups in 1,3-propanediol are located at both ends of the carbon chain, the reticular bridge bond structure formed between the collagen molecules changed into chain-like bridge structure. The bridge bonds between collagen molecules were considered to be weak cross-linking, which was an important reason for the destruction of collagen structure. In this study, the mechanism of interaction between different alcohols and collagen was elucidated, which will be helpful for further development of complex alcohol and collagen products.