The present invention relates to equine amniotic membrane-derived mesenchymal stem cells (eAM-MSCs) and a preparation method thereof. More specifically, the present invention relates to equine amniotic membrane-derived mesenchymal stem cells, which show negative immunological responses to all of the human markers CD19, CD20, CD28, CD31, CD34, CD38, CD41a, CD62L, CD62P and CD200, and positive immunological responses to all of the human markers CD44, CD90 and CD105, and have the ability to be maintained in an undifferentiated state for 14 passages or more and the ability to differentiate into ectoderm, mesoderm and endoderm-derived cells.