Abstract: Animal derived traditional Chinese medicines (ATCMs) are an important part of traditional Chinese medicine (TCM). The lack of proper ideas and strategies made it not systematic and perfect enough on investigating bioactive components and quality evaluation of ATCMs, which restrict many aspects of ATCMs investigation including clinical applications, pharmaceutical technologies, and quality control. Therefore, based on our previous investigations of animal horn and animal derived gelatin TCMs, and the research progress at home and abroad, ideas and strategies for investigating the correlations between proteins/peptides and their bioactivities in animal horn and animal gelatin derived TCMs based on integrated "proteomics/peptidomics-modifications" methods was proposed. Firstly, proteomics and peptidomics analysis can be used to study proteins and peptides in ATCMs. Secondly, modification analysis can be used to reveal those chemical modifications on proteins and peptides of ATCMs. Thirdly, the correlations between components, modifications and traditional bioactivities can be systemic discussed. Based on the present study, hopefully, enough evidences and reference can be provided to resolve the issues in ATCMs investigations on modernization and bioactive material basis.