In this study, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify the structures of peptides in Colla Corii Asini (Ejiao) subjected to simulated gastrointestinal digestion. The peptides were screened for their anti-hypertensive, anti-Alzheimer, and anti-tumor potential by molecular docking. The results showed that 519 active peptides with molecular mass ranging from 661.4 to 2851.4 Da were obtained from the digested products of Ejiao. These peptides were mainly derived from the enzymatic hydrolysis of collagen and hemoglobin. Peptides KGETGLR, SGLDGAKG, and ADGVAGPK were found to have the highest anti-hypertensive, anti-Alzheimer and anti-tumor potential. Hydrogen bond and electrostatic interactions played a vital role in the anti-hypertensive, anti-Alzheimer, and anti-tumor activities of the Ejiao peptides.